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 Received: by mail1.ciwemb.edu with SMTP;7 Oct 1999 07:48:44 -0400 Received: from gilly.gen.cam.ac.uk (131.111.46.170) by mauve.csi.cam.ac.uk with smtp (Exim 3.03 \#1) id 11ZC1u-00023G-00; Thu, 07 Oct 1999 12:48:14 +0100 Received: from gm119 by gilly.gen.cam.ac.uk with local (Exim 1.58 \#2) id 11ZC1p-0000uG-00; Thu, 7 Oct 1999 12:48:09 +0100 To: spradling@XXXX Subject: Helping FlyBase (P-element) - cytology questions. Cc: gm119@XXXX X-Sun-Charset: US-ASCII 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) by mauve.csi.cam.ac.uk with smtp (Exim 3.03 \#1) id 11ZC28-00023Q-00; Thu, 07 Oct 1999 12:48:28 +0100 Received: from gm119 by gilly.gen.cam.ac.uk with local (Exim 1.58 \#2) id 11ZC23-0000uK-00; Thu, 7 Oct 1999 12:48:23 +0100 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
