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Reference
Citation
Spradling, A. (1999.12.9). Helping FlyBase with P-element paper. 
FlyBase ID
FBrf0125024
Publication Type
Personal communication to FlyBase
Abstract
PubMed ID
PubMed Central ID
Text of Personal Communication
From gm119@XXXX Thu Oct 07  12:46:09  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 7 Oct 1999  12:46:09  +0100
To: spradling@XXXX
Subject: Helping FlyBase with P-element paper
Cc: gm119@XXXX
X-Sun-Charset: US-ASCII
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:47:54  +0100
Content-Length: 1835
Dear Allan,
I have curated your P-element paper from Genetics (Genetics 153(1):
135--177) for FlyBase and have several questions about some of the
lines in the various Tables - although given the amount of data in the
paper there are relatively few questions.
I have tried to divide the questions into groups, and I will be sending
each group of questions in a separate e-mail with a different subject
line. Hopefully this will make the questions more manageable and will
stop us getting confused - if you can reply with the same subject line
in the e-mail that would be a great help.
Your answers will be recorded as a personal communication from you to
FlyBase and will be linked to the Genetics paper in FlyBase so that
people can easily see the extra information about the lines in your
paper.
In the following e-mails I have used the following
abbreviations/syntax:
'BFD' signifies the 'Berkeley Fly Database'.
'<up></up>' in allele designations signifies superscript.
I will be sending the following e-mails:
Subject: Helping FlyBase (P-element) - possible typographical errors.
Subject: Helping FlyBase (P-element) - cytology questions.
Subject: Helping FlyBase (P-element) - nomenclature questions.
Subject: Helping FlyBase (P-element) - confirming the identity of alleles.
Subject: Helping FlyBase (P-element) - separable lethals ?
Subject: Helping FlyBase (P-element) - miscellaneous
I look forward to hearing from you,
Gillian
\--------------------------------------------------------------
Gillian Millburn.
FlyBase (Cambridge),
Department of Genetics,
University of Cambridge,
Downing Street, email: gm119@XXXX
Cambridge, CB2 3EH, Ph : 01223-333963
UK. FAX: 01223-333992
\--------------------------------------------------------------
From gm119@XXXX Thu Oct 07  12:46:22  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 7 Oct 1999  12:46:22  +0100
To: spradling@XXXX
Subject: Helping FlyBase (P-element) - cytology questions.
Cc: gm119@XXXX
X-Sun-Charset: US-ASCII
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:48:09  +0100
Content-Length: 8343
Re: P-element paper (Genetics 153(1): 135--177)
Subject: cytology questions.
1. the cytology (as given in FlyBase and the BFD) of the reserve strain
does not match the cytology of the primary strain (I am defining 'does
not match' as any instance where the cytology does not overlap - even
if the cytologies are only a band apart) given in Table 4 or 5. I have
included a table of these below. This is a problem for us because we
do not know where to place the lethal mutation on the chromosome.
In these cases:
a. is the cytology of the reserve line as we have it in FlyBase and the
BFD correct ?
b. Which of the reserve insertions have been verified ?
if the cytology of the reserve lines is correct it seems likely that a
second mutation on the chromosome is what is allelic to the primary
line (at least for the top 2 lines) as the cytology of the inserts is
so different - in that case I will make new alleles that are not
associated with the insertions for the reserve lines. For the others
are the cytologies close enough to presume that they are in the same
gene ?
Primary | cytology of | Reserve | cytology of Reserve |
| primary line | | in FlyBase+BFD |
\--------------------------------------------------------------
l(2)k06502 | 25F3-4 | l(2)02839 | 53B1--2 |
\--------------------------------------------------------------
l(2)k10617 | 27C6-8 | l(2)k11018 | 47C3--4 |
\--------------------------------------------------------------
l(2)k08316 | 58E1-2 | l(2)k08134 | 59B1--2 |
\--------------------------------------------------------------
l(3)02240 | 67C4-5 | l(3)rK145 | 67B4--5 |
\--------------------------------------------------------------
From spradling@XXXX Mon Oct 11  23:16:29  1999
Envelope-to: gm119@XXXX
Delivery-date: Mon, 11 Oct 1999  23:16:29  +0100
Date: 11 Oct 1999  18:15:38  -0400
From: 'Allan Spradling' <spradling@XXXX>
Subject: Re: Helping FlyBase (P-eleme
To: 'Genetics' <gm119@XXXX>
X-Mailer: Mail*Link SMTP-QM 3.0.2
Content-Length: 11905
Reply to: RE>Helping FlyBase (P-element) - cytology questions.
\--------------------------------------
Date: 10/7/99  7:59  AM
To: Allan Spradling
From: Genetics
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To: spradling@XXXX
Subject: Helping FlyBase (P-element) - cytology questions.
Cc: gm119@XXXX
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Message-Id: <E11ZC1p-0000uG-00@XXXX>
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:48:09  +0100
Re: P-element paper (Genetics 153(1): 135--177)
Subject: cytology questions.
1. the cytology (as given in FlyBase and the BFD) of the reserve strain
does not match the cytology of the primary strain (I am defining 'does
not match' as any instance where the cytology does not overlap - even
if the cytologies are only a band apart) given in Table 4 or 5. I have
included a table of these below. This is a problem for us because we
do not know where to place the lethal mutation on the chromosome.
Welcome to the field of cytology. The database reports the data as it was
actually done. Since allelism was not determined until later, it represents
completely unbiased data on cytology. At least a few of the differences are
probably real, since P elements mutating the same gene can be separated by
more than 50kb if the gene is large, and could reside truly in different
bands. Your problem is just to report the data. I note many entries in
Flybase genes where some of the cytology is contradictory. Users understand
that there are errors in localizing breakpoints and in situ sites. It is
worthwhile to look at the cytology of all the P alleles of a gene when there
are more than 2. Often, only one is an outlier. We have redone some of these
when the discrepancy was large and corrected the data in earlier versions of
the database. Other differences we consider too minor to worry about.
In these cases:
a. is the cytology of the reserve line as we have it in FlyBase and the
BFD correct ?
Usually, but you do not have the latest version of the P element database and
a few corrections were made.
b. Which of the reserve insertions have been verified ?
All reserve insertions of lines with a phenotype are verified.
if the cytology of the reserve lines is correct it seems likely that a
second mutation on the chromosome is what is allelic to the primary
line (at least for the top 2 lines) as the cytology of the inserts is
so different - in that case I will make new alleles that are not
associated with the insertions for the reserve lines. For the others
are the cytologies close enough to presume that they are in the same
gene ?
Primary | cytology of | Reserve | cytology of Reserve |
| primary line | | in FlyBase+BFD |
\--------------------------------------------------------------
l(2)k06502 | 25F3-4 | l(2)02839 | 53B1--2 (error) | l(2)02839 is
not 53B1-2; this was a mixup with 02836 which is at that site
\--------------------------------------------------------------
l(2)k10617 | 27C6-8 | l(2)k11018 | 47C3--4 (error) | l(2)k11018 is
at 27D1-2
\--------------------------------------------------------------
l(2)k08316 | 58E1-2 | l(2)k08134 | 59B1--2 | one of two
must be wrong, not resolved
\--------------------------------------------------------------
l(3)02240 | 67C4-5 | l(3)rK145 | 67B4--5 | not certain
that rK145 is actually an allele of l(3)02240; retained in reserve due to
possible geentic interaction; someone studying this locus will have to figure
this out-
\--------------------------------------------------------------
From gm119@XXXX Thu Oct 07  12:46:36  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 7 Oct 1999  12:46:36  +0100
To: spradling@XXXX
Subject: Helping FlyBase (P-element) - confirming the identity of alleles.
Cc: gm119@XXXX
X-Sun-Charset: US-ASCII
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:48:23  +0100
Content-Length: 1818
Re: P-element paper (Genetics 153(1): 135--177)
Subject: confirming the identity of alleles.
1. fs(2)10089 is presumably either hts1 or hts2 as you give the
reference FBrf0056130 == Yue and Spradling, 1992, Genes Dev. 6:
2443--2454 for this line and both hts1 and hts2 are described in
this reference. Do you know which allele fs(2)10089 corresponds to ?
From spradling@XXXX Thu Oct 21  15:56:18  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 21 Oct 1999  15:56:18  +0100
Date: 21 Oct 1999  10:56:38  -0400
From: 'Allan Spradling' <spradling@XXXX>
Subject: Re: Helping FlyBase (P-eleme
To: 'Genetics' <gm119@XXXX>
X-Mailer: Mail*Link SMTP-QM 3.0.2
Content-Length: 3275
Reply to: RE>Helping FlyBase (P-element) - confirming the identity
of...
\--------------------------------------
Date: 10/7/99  7:59  AM
To: Allan Spradling
From: Genetics
Received: by mail1.ciwemb.edu with SMTP;7 Oct 1999  07:48:58  -0400
Received: from gilly.gen.cam.ac.uk (131.111.46.170)
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To: spradling@XXXX
Subject: Helping FlyBase (P-element) - confirming the identity of alleles.
Cc: gm119@XXXX
X-Sun-Charset: US-ASCII
Message-Id: <E11ZC23-0000uK-00@XXXX>
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:48:23  +0100
Re: P-element paper (Genetics 153(1): 135--177)
Subject: confirming the identity of alleles.
1. fs(2)10089 is presumably either hts1 or hts2 as you give the
reference FBrf0056130 == Yue and Spradling, 1992, Genes Dev. 6:
2443--2454 for this line and both hts1 and hts2 are described in
this reference. Do you know which allele fs(2)10089 corresponds to ?
Yes. fs(2)10089 is hts2 and is from the Karpen and Spradling, 1992 screen;
hts1 was recovered from the from a small pilot screen the preceeded the K
and S screen- its original name was fs(2)PZ276.
From gm119@XXXX Thu Oct 07  12:46:47  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 7 Oct 1999  12:46:47  +0100
To: spradling@XXXX
Subject: Helping FlyBase (P-element) - miscellaneous
Cc: gm119@XXXX
X-Sun-Charset: US-ASCII
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:48:34  +0100
Content-Length: 1804
Re: P-element paper (Genetics 153(1): 135--177)
Subject: miscellaneous
l(2)01528 and l(2)05287.
we currently have two lethals assigned to the 'l(2)01528' chromosome -
one which we think is allelic to l(2)05287 and one which is not - which
we call l(2)39Ea01528. These have been created because of problems
with the complementation data in the original P-element file we got
from Berkeley. Please could you send me all the information you have
about the following 4 lines in terms of their complementation with
regard to each other, complementation with deficiencies, existence of
secondary lethals etc., so that I can sort out what to do with these
lines. The lines are:
l(2)01528
l(2)05287
l(2)k16804B
l(2)k08613
From spradling@XXXX Fri Oct 29  19:12:44  1999
Envelope-to: gm119@XXXX
Delivery-date: Fri, 29 Oct 1999  19:12:44  +0100
Date: 29 Oct 1999  14:13:01  -0400
From: 'Allan Spradling' <spradling@XXXX>
Subject: Re: Helping FlyBase (P-eleme
To: 'Genetics' <gm119@XXXX>
X-Mailer: Mail*Link SMTP-QM 3.0.2
Content-Length: 4751
Reply to: RE>Helping FlyBase (P-element) - miscellaneous
>Subject: miscellaneous
l(2)01528 and l(2)05287.
we currently have two lethals assigned to the 'l(2)01528' chromosome -
one which we think is allelic to l(2)05287 and one which is not - which
we call l(2)39Ea01528. These have been created because of problems
with the complementation data in the original P-element file we got
from Berkeley. Please could you send me all the information you have
about the following 4 lines in terms of their complementation with
regard to each other, complementation with deficiencies, existence of
secondary lethals etc., so that I can sort out what to do with these
lines. The lines are:
l(2)01528
l(2)05287
l(2)k16804B
l(2)k08613
I don't see any problem with the complementation data. There are two separate
complementation groups:
l(2)01528 includes: l(2)k13715 , l(2)k08922, l(2)k08613
and
l(2)05287 includes: l(2)k16804b
we have no evidence of any overlap between these sets of alleles: l(2)05287
noncomplements only l(2)k16804b and complements l(2)01528
l(2)01528 only noncomplements members of its complementation group; both
complement various deficiencies.
From gm119@XXXX Thu Oct 07  12:46:44  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 7 Oct 1999  12:46:44  +0100
To: spradling@XXXX
Subject: Helping FlyBase (P-element) - separable lethals ?
Cc: gm119@XXXX
X-Sun-Charset: US-ASCII
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:48:29  +0100
Content-Length: 4476
Re: P-element paper (Genetics 153(1): 135--177)
Subject: separable lethals ?
This e-mail is about lines whose prefix (e.g. 'v(2)' ) in Tables 4 and
5 differs from what we have in FlyBase, so there may be separable
second site lethals on the chromosome.
1. Lines which have the prefix 'n(2)' or 'n(3)' in Tables 4 and 5, but
are currently listed as 'l(2)' or 'l(3)' in FlyBase. For each of these
lines could you please confirm whether the original line was lethal
when isolated i.e. is there a secondary lethal mutation on the
chromsome which is separable from the insertion. Any information you
have about the position of these secondary lethals on the chromosome
would also be very useful. The lines are:
n(2)k04512
n(2)05337
n(2)06253
n(2)k04810
n(2)k07110
n(2)k07332
n(2)k09217
n(2)k13807
n(2)k17003
n(2)k07245
n(3)s2681
n(3)01949
n(3)03884
n(2)k09033
n(2)k07236
reserve lines:
n(2)k11702
n(2)k09303
n(2)k10209
2. lines which are 'v(2)' or 'v(3)' in Tables 4 and 5 but currently
listed as lethals in FlyBase. Please can you confirm for each line
whether the original line was lethal when isolated i.e. is there a
secondary lethal mutation on the chromsome which is separable from the
insertion which is causing the visible phenotype. Again, any
information on the location of the secondary lethal would be helpful.
v(2)k09107
v(2)rG232
v(2)k06408
v(2)k03514
v(2)k16105
v(2)k15606
v(3)03847
Reserve:
v(2)k11209
v(2)k15819
3. n(2)09967 - this is given the prefix n(2) in Table 4 but is listed
as ms(2) in FlyBase. Please could you confirm whether the original
line was male sterile when isolated i.e. is there a secondary male
sterile mutation on the chromosome separable from the insertion.
4. n(3)05241 - we have this as an allele of Hsromega (FBgn0001234)
which is stated to be semilethal.
Do you have any evidence that the insertion is in Hsromega - the reason
we have it as an allele of Hsromega is that in the original data we got
from Berkeley for the P-element project it states that the insert is in
Hsromega, is this still true (as in Table 5 you do not say that
n(3)05241 is in Hsromega) ?
Does the semi-lethality of the chromosome map to Hsromega or elsewhere
\- I think the latter given that you have given it an 'n(3)' designation
and the P-element maps to the same place as Hsromega, and there is also
a line in the BFD ' the semilethality maps elsewhere and can be
recombined off (Pardue Aug 1998) '. Any info on the location of the
semi-lethality (if separate) would be great.
5. ms(3)08724 - we have l(3)08724 in FlyBase. Please could you confirm
whether there is a secondary lethal on the chromosome which is separate
from the male sterility caused by the insertion.
6. lines which are 'fs(2)' or 'fs(3)' in Tables 4 and 5 but currently
listed as lethals in FlyBase. Please can you confirm for each line
whether the original line was lethal when isolated i.e. is there a
secondary lethal mutation on the chromsome which is separable from the
insertion which is causing the female sterility phenotype. Again, any
information on the location of the secondary lethal would be helpful.
fs(2)k09833
fs(2)k10816
7. v(2)rJ571. The insertion is in osp. In FlyBase we have that this
allele is semi-lethal. Is there a separable semi-lethal on the
chromosome ?
8. n(2)k10237
is there a secondary lethal on this chromosome (as above) ?
The reserve line for this is stated to be 'l(2)k16510'.
What is the basis of the statement of allelism of n(2)k10237 and
l(2)k16510 given that n(2)k10237 has no phenotype ?
Has l(2)k16510 been verified (i.e. does the insert cause the lethality)
or is there a secondary lethal on the chromosome ?
From spradling@XXXX Wed Dec 08  23:16:19  1999
Envelope-to: gm119@XXXX
Delivery-date: Wed, 8 Dec 1999  23:16:19  +0000
Date: 8 Dec 1999  18:13:57  -0500
From: 'Allan Spradling' <spradling@XXXX>
Subject: Re: Helping FlyBase (P-eleme
To: 'Genetics' <gm119@XXXX>
X-Mailer: Mail*Link SMTP-QM 3.0.2
Content-Length: 4655
Reply to: RE>Helping FlyBase (P-element) - separable lethals ?
Lines indicated below as 'l' were changed from l(2) or l(3) to n(2) or n(3)
when complementation studies with deficiencies or other P element lines
indicated that the P element had no associated phenotype. We did not attempt
to map the associated lethal(s) on the original chromosome and consider them
irrelevant. If we happen to cross off the background lethality we will
substitute the clean stock, just as one would for any other stock that arrived
with a background mutation on it. I do not guarantee that any of these stocks
still have a background lethal on them. The lines were isolated because of
their P elements, not because of the lethals. It should be noted that the
indicated stock may contain a background mutation on the P element-bearing
chromosome. All were saved because molecular analysis indicates that the P
elements disrupt an interesting transcript or open-reading frame.
n(2)k04512 l
n(2)05337 l
n(2)06253 l
n(2)k04810 l
n(2)k07110 l
n(2)k07332 l
n(2)k09217 l
n(2)k13807 l
n(2)k17003 l
n(2)k07245 l
n(3)s2681 l
n(3)01949 l designation of n is based on placement of B52 to left of
insertion by cytology
n(3)03884 l
n(2)k09033 l
n(2)k07236 l ; should probably be v(2), since there is a very weak eye
phenotype over Df(2R)Jp1
reserve lines:
n(2)k11702 l ; note, not tested for sterility over Df, so n designation
provisional
n(2)k09303 l
n(2)k10209 l
2. lines which are 'v(2)' or 'v(3)' in Tables 4 and 5 but currently
listed as lethals in FlyBase. Please can you confirm for each line
whether the original line was lethal when isolated i.e. is there a
secondary lethal mutation on the chromsome which is separable from the
insertion which is causing the visible phenotype. Again, any
information on the location of the secondary lethal would be helpful.
v(2)k09107 l
v(2)rG232 l
v(2)k06408 l
v(2)k03514 l my record says this should be n(2)
v(2)k16105 l
v(2)k15606 l
v(3)03847 l
Reserve:
v(2)k11209 l
v(2)k15819 l
3. n(2)09967 - this is given the prefix n(2) in Table 4 but is listed
as ms(2) in FlyBase. Please could you confirm whether the original
line was male sterile when isolated i.e. is there a secondary male
sterile mutation on the chromosome separable from the insertion.
Castrillon et al. stated was allelic to ms(2)42D, but was not male sterile
over a Df for region; I did not test to see if both lines had the same
background male sterile
4. n(3)05241 - we have this as an allele of Hsromega (FBgn0001234)
which is stated to be semilethal.
Do you have any evidence that the insertion is in Hsromega - the reason
we have it as an allele of Hsromega is that in the original data we got
from Berkeley for the P-element project it states that the insert is in
Hsromega, is this still true (as in Table 5 you do not say that
n(3)05241 is in Hsromega) ?
No. Insertion is located upsream from hsr-omega and the pardue lab did not
find that the insertion disrupted the gene;
Does the semi-lethality of the chromosome map to Hsromega or elsewhere
\- I think the latter given that you have given it an 'n(3)' designation
and the P-element maps to the same place as Hsromega, and there is also
a line in the BFD ' the semilethality maps elsewhere and can be
recombined off (Pardue Aug 1998) '. Any info on the location of the
semi-lethality (if separate) would be great.
Yes, our data agrees with Pardue.
5. ms(3)08724 - we have l(3)08724 in FlyBase. Please could you confirm
whether there is a secondary lethal on the chromosome which is separate
from the male sterility caused by the insertion.
I have no record of any lethality associated with this stock.
6. lines which are 'fs(2)' or 'fs(3)' in Tables 4 and 5 but currently
listed as lethals in FlyBase. Please can you confirm for each line
whether the original line was lethal when isolated i.e. is there a
secondary lethal mutation on the chromsome which is separable from the
insertion which is causing the female sterility phenotype. Again, any
information on the location of the secondary lethal would be helpful.
fs(2)k09833 l
fs(2)k10816 l
7. v(2)rJ571. The insertion is in osp. In FlyBase we have that this
allele is semi-lethal. Is there a separable semi-lethal on the
chromosome ?
It was semi-lethal in our tests; I have no evidence that the semi-lethality is
separable. Calling a line v(2) does not address the question of
semilethality.
8. n(2)k10237
is there a secondary lethal on this chromosome (as above) ? Yes
The reserve line for this is stated to be 'l(2)k16510'.
What is the basis of the statement of allelism of n(2)k10237 and
l(2)k16510 given that n(2)k10237 has no phenotype ?
Simply the fact that the P elements in these lines are inserted 7bp apart.
Obvioously, they are not allelic in a strict genetic sense. However, we need
some way to indicate this molecular definition of allelism. Many such line
pairs will eventually be found to share a subtle phenotype, such as an effect
on the production of some transcript.
Has l(2)k16510 been verified (i.e. does the insert cause the lethality)
or is there a secondary lethal on the chromosome ? Both lines must have
secondary lethals, otherwise their lethality would not complement.
From gm119@XXXX Thu Oct 07  12:46:15  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 7 Oct 1999  12:46:15  +0100
To: spradling@XXXX
Subject: Helping FlyBase (P-element) - possible typographical errors.
Cc: gm119@XXXX
X-Sun-Charset: US-ASCII
From: Gillian Millburn (Genetics) <gm119@XXXX>
Date: Thu, 7 Oct 1999  12:48:02  +0100
Content-Length: 3042
Re: P-element paper (Genetics 153(1): 135--177)
Subject: possible typographical errors.
1. in the entry for the l(3)05014 line, the deficiency '29' (Df(3L)Cat)
appears in both the Non-comp and Comp columns of the Table - which is
correct ?
2. in the entry for the l(3)06743 line, the deficiency '64'
(Df(3R)01215) appears in both the Non-comp and Comp columns of the
Table - which is correct ?
3. in the entry for the l(3)07207 line, the deficiency '58'
(Df(3R)crb87-4) appears in both the Non-comp and Comp columns of the
Table - which is correct ?
4. for line l(3)01688, the same designation is in the reserve column.
Could you tell me what the reserve line is for l(3)01688.
From spradling@XXXX Thu Dec 09  15:33:09  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 9 Dec 1999  15:33:09  +0000
Date: 9 Dec 1999  10:30:45  -0500
From: 'Allan Spradling' <spradling@XXXX>
Subject: Re: Helping FlyBase (P-eleme
To: 'Genetics' <gm119@XXXX>
X-Mailer: Mail*Link SMTP-QM 3.0.2
Content-Length: 6231
Reply to: RE>Helping FlyBase (P-element)
Subject: possible typographical errors.
1. in the entry for the l(3)05014 line, the deficiency '29' (Df(3L)Cat)
appears in both the Non-comp and Comp columns of the Table - which is
correct ?
Non-comp is correct. The other entry was from a much earlier experiment with
a Df(3L)Cat stock that we now presume was bad. This should not have been in
the comp table
2. in the entry for the l(3)06743 line, the deficiency '64'
(Df(3R)01215) appears in both the Non-comp and Comp columns of the
Table - which is correct ?
We ment to only have the non-comp entry. However, the line is only
semi-lethal and it is a difficult call. This might be a leadky allele of
l(3)01235.
3. in the entry for the l(3)07207 line, the deficiency '58'
(Df(3R)crb87-4) appears in both the Non-comp and Comp columns of the
Table - which is correct ?
non-comp is correct.
4. for line l(3)01688, the same designation is in the reserve column.
Could you tell me what the reserve line is for l(3)01688.
reserve line is fs(3)02003
From ma11@XXXX Thu Nov 25  19:00:03  1999
Envelope-to: gm119@XXXX
Delivery-date: Thu, 25 Nov 1999  19:00:03  +0000
To: spradling@XXXX
Subject: Help Michael Please
Cc: ma11XXXX, ag24XXXX,
gm119XXXX, gerryXXXX
X-Sun-Charset: US-ASCII
From: Michael Ashburner (Genetics) <ma11@XXXX>
Date: Thu, 25 Nov 1999  19:02:13  +0000
Content-Length: 465
Allan
I have just finished annotating your new genes in Table 7 and
putting in the correct database cross-references to 'homologs' and GO.
There are several accession numbers in the right hand column which must be wrong
\- they are neither GenBank nor SwissProt accession numbers. Can you help
determining what they should have been please ?
Michael
===========================
Aats-ile I59314
Dhh1 1431254
Hrr25 1370424
Msp1 1323004
Zfrp8 should be: U10903
>From spradling@XXXX Sun Nov 28  16:15:49  1999
Envelope-to: ma11@XXXX
Delivery-date: Sun, 28 Nov 1999  16:15:49  +0000
Date: 26 Nov 1999  16:11:43  -0500
From: 'Allan Spradling' <spradling@XXXX>
Subject: Re: Help Michael Please
To: 'Genetics' <ma11@XXXX>
X-Mailer: Mail*Link SMTP-QM 3.0.2
Content-Length: 5587
Reply to: RE>Help Michael Please
Hi Michael,
I presume that these are protein database numbers, because these matches were
found by BLASTX type searches. Here is what I could come up with from the
highly truncated BLAST output records that were saved from the searches:
===========================
>Aats-ile I59314
sp|P41252|SYI_HUMAN ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (ISOLEUCINE--TRNA
LIGASE) (ILERS) pir||I59314 Isoleucyl tRNA Synthetase - human gnl|PID|d1006382
(D28473) isoleucyl-tRNA synthetase <up>Homo sapiens</up> Length = 1266
>Dhh1 1431254
LOCUS SCRNAH 1824 bp DNA PLN 17-AUG-1993
DEFINITION S.cerevisiae gene for RNA-helicase.
ACCESSION X66057
NID g4352
VERSION X66057.1  GI:4352 
KEYWORDS helicase.
SOURCE baker's yeast.
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales;
Saccharomycetaceae; Saccharomyces.
REFERENCE 1 (bases 1 to 1824)
AUTHORS Strahl-Bolsinger,S.
TITLE Direct Submission
JOURNAL Submitted (13-MAY-1992) S. Strahl-Bolsinger, Universitaet
Regensburg, Lehrstuhl fuer Zellbiologie und Pflanzen,
Universitaetsstrasse 31, Postfach 397, 8400 Regensburg, FRG
REFERENCE 2 (bases 1 to 1824)
AUTHORS Strahl-Bolsinger,S. and Tanner,W.
TITLE A yeast gene encoding a putative RNA helicase of the 'DEAD'-box
family
JOURNAL Yeast 9 (4), 429-432 (1993)
MEDLINE 93289822
FEATURES Location/Qualifiers
source 1..1824
/organism='Saccharomyces cerevisiae'
/db_xref=' taxon:4932 '
/clone_lib='lambda gt11 genomic'
gene 198..1718
/gene='DHH1'
CDS 198..1718
/gene='DHH1'
/codon_start=1
/product='RNA-helicase of the DEAD-BOX family'
/protein_id='CAA46853.1'
/db_xref=' PID:g4353 '
/db_xref=' GI:4353 '
/db_xref='SWISS- PROT:P39517 '
/translation='MGSINNNFNTNNNSNTDLDRDWKTALNIPKKDTRPQTDDVLNTK
GNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVI
PTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR
LNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPP
THQSLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNT
LFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKV
RTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDR
FNLYKIEQELGTEIAAIPATIDKSLYVAENDETVPVPFPIEQQSYHQQAIPQQQLPSQ
QQFAIPPQQHHPQFMVPPSHQQQQAYPPPQMPSQQGYPPQQEHFMAMPPGQSQPQY'
BASE COUNT 598 a 362 c 321 g 543 t
>Hrr25 1370424
a search on the EST (LD08007) yields matches to the amino terminus of many
CK-1 related genes (see below). In a previous search, Hrr25 gave the best
match, but I don't see it now and it seems likely that the gene name should be
something more general, such as 'CKI-related'
emb|CAB60309.1| (AL032656) similar to Eukaryotic protein ki... 140 2e-32
sp|Q62763|KC13_RAT CASEIN KINASE I, GAMMA 3 ISOFORM (CKI-GA... 140 2e-32
sp|Q62761|KC11_RAT CASEIN KINASE I, GAMMA 1 ISOFORM (CKI-GA... 140 2e-32
ref|NP_004375.1|PCSNK1G3| casein kinase 1, gamma 3 >gi|4590... 139 5e-32
gb|AAD26526.1|AF049090_1 (AF049090) casein kinase I gamma 3... 139 5e-32
sp|P35509|KC13_BOVIN CASEIN KINASE I, GAMMA 3 ISOFORM (CKI-... 138 1e-31
ref|NP_001310.1|PCSNK1G2| casein kinase 1, gamma 2 >gi|3024... 135 5e-31
sp|Q62762|KC12_RAT CASEIN KINASE I, GAMMA 2 ISOFORM (CKI-GA... 127 2e-28
example:
sp|Q62763|KC13_RAT CASEIN KINASE I, GAMMA 3 ISOFORM (CKI-GAMMA 3)
>gi|1363273|pir||C56711 casein kinase I (EC 2.7.1.)
gamma-3 - rat >gi|854737 (U22321) casein kinase 1 gamma 3
isoform <up>Rattus norvegicus</up>
Length = 448
Score = 140 bits (349), Expect = 2e-32
Identities = 66/89 (74%), Positives = 79/89 (88%)
Frame = +1
Query: 814 KSSSNNMYSTRQSVSTTTGVLMVGPNFRVGKKIGCGNFGELRLGKNLYNNEHVAIKMEPM 993
+ S + +STR + S+++GVLMVGPNFRVGKKIGCGNFGELRLGKNLY NE+VAIK+EPM
Sbjct: 17 RPSGRSGHSTRGTGSSSSGVLMVGPNFRVGKKIGCGNFGELRLGKNLYTNEYVAIKLEPM 76
Query: 994 KSKAPQLHLEYRFYKLLGSHAEGVPEVYY 1080
KS+APQLHLEYRFYK LGS +G+P+VYY
Sbjct: 77 KSRAPQLHLEYRFYKQLGS-GDGIPQVYY 104
Msp1 1323004
sp|P54815|MSP1_CAEEL MSP1 PROTEIN HOMOLOG >gi|3878242|emb|CAA93516.1|
(Z69664) Similarity
to Yeast MSP1 protein (TAT-binding homolog 4)
( SW:MSP1_YEAST ) <up>Caenorhabditis elegans</up>
Length = 357
Score = 272 bits (687), Expect = 6e-72
Identities = 139/311 (44%), Positives = 214/311 (68%), Gaps = 15/311 (4%)
Frame = +1
Query: 109 KGQIFQVLVRLSVASLITYYSVKWMMNQMDPTSKNKKKAKVLAEEQLKRLAEQEGFKLRG 288
+ ++ V +R+ A+ +++ SV++++ +DP +++K +++ \*+L + G R
Sbjct: 4 RNELIGVAIRVVAAAAVSFLSVRYLVKYLDPNYSVNEESK----KKVAQLFHELGID-RQ 58
Query: 289 QEFSDYELMIASHLVVPADITVSWADIA---------------GLDSVIQELRESVVLPI 423
E S++E+ IA+ V D+ W \*+I G + ++ EL++ ++LP+
Sbjct: 59 IELSEHEIRIATQFVGGEDVGADWDEIGRTENCFAKKKKNFTGGCEELVAELKDRIILPL 118
Query: 424 QHKDLFKHSKLWQAPKGVLLHGPPGCGKTLIAKATAKEAGMRFINLDVAILTDKWYGESQ 603
+ S L P+G+LL+GPPGCGKTL+AKA A+ AG RFINL V+ LTDKWYGESQ
Sbjct: 119 RFASQ-SGSHLLSPPRGILLYGPPGCGKTLLAKAVARAAGCRFINLQVSNLTDKWYGESQ 177
Query: 604 KLTSAVFSLASRIEPCIIFIDEIDSFLRSRNMNDHEATAMMKTQFMMLWDGLSTNANSTV 783
KL +AVFS+A + \*+P IIFIDEIDSFLR R +DHE+TAMMK QFM LWDG S++ + +
Sbjct: 178 KLAAAVFSVAQKFQPTIIFIDEIDSFLRDRQSHDHESTAMMKAQFMTLWDGFSSSGDQ-I 236
Query: 784 IVMGATNRPQDLDKAIVRRMPAQFHIGLPSETQRKDILKLILQSEEVSQDVDLNRLSKLT 963
IVMGATNRP+D+D AI+RRM A+F + +P+ QR IL +IL++E+++ V+L +++
Sbjct: 237 IVMGATNRPRDVDAAILRRMTARFQVPVPNAKQRSQILNVILRNEKINNTVNLGEIAQAA 296
Query: 964 NGFSGSDLREMCRNASVYRMRQLITS 1041
G SGSDL+E+CR A + R + + S
Sbjct: 297 EGLSGSDLKEVCRLALLARAKATVAS 322
Zfrp8 should be: U10903
this was a typo truncation, as can been seen by inspection of the table
DOI
Related Publication(s)
Research paper
The Berkeley Drosophila genome project gene disruption project. Single P-element insertions mutating 25% of vital Drosophila genes.
Spradling et al., 1999, Genetics 153(1): 135--177 [FBrf0111489]
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