From smount@XXXX Wed Apr 05 19:37:01 2000
Date: Wed, 5 Apr 2000 14:41:28 -0400 (EDT)
From: Stephen M Mount <smount@XXXX>
To: Michael Ashburner <ma11@XXXX>
Subject: RE: drosophila snRNAs (fwd)
Message-ID: <Pine.GSO.4.21.0004051440480.10337-100000@XXXX>
Michael,
This is what I sent to Celera for the annotation. The Excel file is being
sent separately.
Steve
---------- Forwarded message ----------
Date: Mon, 28 Feb 2000 21:16:48 -0500 (EST)
From: Stephen M Mount <smount@XXXX>
To: 'Skupski, Marian P.' <Marian.Skupski@XXXX>
Subject: RE: drosophila snRNAs
Marian,
This email contains, in the body of the text, NOT as attachments,
1) established Drosophila snRNA sequences for U1, U2, U4, U5 and U6
2) hypothetical Drosophila snRNA sequences for U4atac, U6atac and U12
3) updated versions of the summary files I sent yesterday
The latter includes the three additional U2 genes that were missing
yesterday.
You may want to correlate these with existing (published) snRNA genes
for U1, U2, U4 and U6.
Note also that I found U5 genes that have variant 3' termini and may not
be real genes at all.
I hope this does it for you. If not, feel free to contact me again.
Steve Mount
\##################################################
1) established Drosophila snRNA sequences for U1, U2, U4, U5 and U6
What follows are established Drosophila snRNA sequences; most are based on
RNA sequencing. U3 is not a spliceosomal RNA, and I did not investigate
it.
> U1 RNA ACCESSION X04257
atacttacctggcgtagaggttaaccgtgatcacgaaggcggttcctccggagtgaggcttggccattgcacctcggctg
agttgacctctgcgattattcctaatgtgaataactcgtgcgtgtaatttttggtagccgggaatggcgttcgcgccgtc
ccga
>U2 RNA
atcgcttctcggccttatggctaagatcaaagtgtagtatctgttcttatcagcttaacatctgatagttcctccattgg
aggacaacaaatgttaaactgatttttggaatcagacggagtgctaggggcttgctccacctctgtcgcgggttggcccg
gtattgcagtaccgccgggatttcggcccaac
>U4 RNA ACCESSION K03095
agcttagcgcagtggcaataccgtaaccaatgaagcctccctgaggtgcggttattgctagttgaaaactttaaccaacc
cacgccatgggacgtgaaataccgtccactacggcaatttttggaagcccttacgagggctaa
> U5 RNA. ACCESSION K03096
atactctggtttctcttcaatgtcgaataaatctttcgccttttactaaagatttccgtggagaggaacactctaagagt
ctaaaactaattttttagtcagtcttgtcgcaagactggggcca
> U6 RNA. ACCESSION X06669
gttcttgcttcggcagaacatatactaaaattggaacgatacagagaagattagcatggccccagcgcaaggatgacacg
caaaatcgtgaagcgttccacattttt
\##################################################
2) hypothetical Drosophila snRNA sequences for U4atac, U6atac and U12
What follows are HYPOTHETICAL Drosophila snRNA sequences; based on the
genomic sequence. I found these with blast searches using modified
parameters.
> hypothetical fly U4atac; What's depicted here is the region of
similariy; the actual RNA may extend beyond these nucleotides.
accttccttgtcttggggagcagaaatgttcaatgaacgtctagtgaggacattgctgctgacaccaatgatgacacccc
cgctcgccgatcgttcgcgattggagttcggaatttttgga
> hypothetical fly U6atac;
gtggtccaaacgtgttgtttggaaggagagcaagttagcactcccctagacaaggatggaacacataaacggtcggctag
gcacagacaaaagccgtccacaaattttt
> hypothetical fly U12 RNA; matches vertebrate U12 snRNA at both
ends. gtgcctcaaactaatgagtaaggaaaaccaatcagccttgctaatcgcttggcagtattggcttctaggcaggg
gggcgt
gtcccgcgccccttgaagctcaaatttttgcaagggcacaggtcgtcccctcctcctccgcgtgggtggcgttcggccga
gcgaaccggcgcctactttgcgtccggctagcgaggatctctgggtgccatcccacggctgggtgttgcgatctgccc
Support for U4atac:
gb|AC013956.1|AC013956 Drosophila melanogaster, \*** SEQUENCING IN
PROGRESS \***, in ordered
pieces
Length = 65679
Score = 52.1 bits (116), Expect = 5e-06
Identities = 88/129 (68%), Gaps = 13/129 (10%)
Strand = Plus / Minus
Query: 2 accatccttttcttggggttgcgctactgtccaatgagcgcatagtgagggcagtactgc
61
||| ||||| |||||||| || | ||| |||||| || |||||||| || | ||||
Sbjct: 1325 accttccttgtcttgggga-gcagaaatgttcaatgaacgtctagtgaggacattgctgc
1267
Query: 62 taacgcc--tgaacaacacacccgcatcaactagagcttttgc---tttattttggtgca
116
| || || || | |||| ||||| || | || | || || | | || || |
Sbjct: 1266 tgacaccaatg-atgacacccccgc-tcgcc--gatcgttcgcgattggagttcgg---a
1214
Query: 117 atttttgga 125
|||||||||
Sbjct: 1213 atttttgga 1205
\##################################################
3) updated versions of the summary files I sent yesterday
snRNA promoter hits:
AC018327.1C taattcccaactagttctagttgcgccctcatggaaa U1-82.3 001
AC015109.1C caattcccaactggttttagctgctcagccatggaaa U1-95.1 002
AC019896.1C caattcccaactgcttctggccgtttgctcatggaag U2 003
AC019896.1C gaattcccaactgcttctggccgtttggtcatggaag U2 004
AC015154.1C taattcccaactggttctggctacttccctatggaga U1-95.2 005
AC015154.1C aaattcccaaacagttctggcagatctctcaaggaga U1-95.3 006
AC017493.1C taattcccaactgcttctggccatcagctcatggaaa U1-21.1 007
AC019965.1C taattcccaaatggttctggccgtttgcccatcgaga U2 008
AC015392.1C taattcccaactgctactggctgcgcttgcatggagt ?? 009
AC017832.1C taattcccaaatggttctggcttgctgtgaatggaat U4-1 010
AC014745.1C taattcccaactgcttctggcagcgccggcatggtat U4-2 011
AC019965.1C tgattcccaacatgttcaagctcgttctaaatgatcg U5 012
AC019603.1C taattcccaacgtgttaaagcagtcactgaatagagt U5 (RNA) 017
AC019905.1C gaattcccaaaaagttctatcacagaacgaatctagg U5 018
AC017727.1C tgattcccaacacgttcaagcaatttcttagtggtac U5 019
AC019732.1C aaattcccaactccttctggccaacactgatcctaga U5 var. 020
AC017832.1C taattcccaagcggttctattcaatattgagtatgga U5 var. 021
AC017832.1C aaattcccaattccttctggccaatactgatcctaga U5 var. 022
AC014181.1C tgattcccaaccggttctggttgcatggccatgagtt U12 013
AC018038.1C tgattcccaagtacatattctgcaagagtacagtata U6-1 014
AC018038.1C taattctcaactgctctttcctgatgttgatcattta U6-2 015
AC018038.1C taattctcaacttctttttccagactcagttcgtata U6-3 016
AC018217.1C aaattcccaagttctttttccgcatggagtgcttata U6atac 023
AC013956.1C taattcccaactagtactggccacttttgcttgaggt U4atac 024
AC017832.1C taattcccaactgattttagctgcagtcgcatgaagt U2 025
AC017832.1C taattctcaactgattttagctgcagtcgcatgaagt U2 026
AC019732.1C taattcccaactggtcttggctgcagtcgcatcaagt U2 027
Small nuclear RNA gene report. 2-28-00
I found 5 genes for U1, 6 genes for U2, 2 genes for U4, 7 genes for U5 (3
of which are quite divergent at the 3' end), 3 genes for U6, 1 gene for
U12, 1 gene for U6atac and 1 gene for U4atac.
Sequences for Drosophila U1, U2, U4, U5 and U6 RNAs were known. Finding
the genes for U4atac, U6atac and U12 absolutely required varying the blast
search parameters. -r 10 -q -11 -W 7 -G 15 -E 4; -r 7 -q -14 -W 7
-G 7 -E 3; and -r 4 -q -5 -W 8 -G 10 -E 2 were among the more
successfull parameter sets.
Details follow below. Unfortunately, I did these searches through GenBank,
and so I have GenBank accession numbers rather than Celera numbers.
That these are indeed snRNA genes is clear from their promoter
sequences. ALL of these genes have a characteristic snRNA promoter
properly placed upstream of the RNA, so I have a high confidence in
them. I do not mention U11 because I could not find anything that was
compelling; the nature of snRNA conservation is such that I could be
missing something.
U1 -- five genes, all of which were previously described:
gb|AC018327.1|AC018327 Drosophila melanogaster, \*** SEQUENC... 327
8e-89
my 001; U1-82.3
gb|AC017493.1|AC017493 Drosophila melanogaster, \*** SEQUENC... 311
5e-84
my 007; U1-21.1
gb|AC015109.1|AC015109 Drosophila melanogaster, \*** SEQUENC... 311
5e-84
my 002; U1-95.1
gb|AC015154.1|AC015154 Drosophila melanogaster, \*** SEQUENC... 311
5e-84
my 005; U1-95.2
my 006; U1-95.3
Additional U1-related sequences at 82E: 82.1 and a pseudogene (82.2) are
missing.
Their absence may be a polymorphism (due to recombination); the published
sequences of the real genes, 82.1 and 82.3 are identical, and they were
known to be directly oriented on the phage clone.
Alternatively, the tandem repeat could have caused an assembly error.
U2 -- six genes and what it probably a pseudogene. I have yet to work out
the relationship between these genes and what was previously published.
gb|AC019896.1|AC019896 Drosophila melanogaster, \*** SEQUENC... 381
e-105
2 genes (my 003, 004)
gb|AC019965.1|AC019965 Drosophila melanogaster, \*** SEQUENC... 373
e-102
gb|AC017832.1|AC017832 Drosophila melanogaster, \*** SEQUENC... 373
e-102
2 genes (my 025, 026). There is also a U4 gene and two U5 genes in
this contig.
gb|AC019732.1|AC019732 Drosophila melanogaster, \*** SEQUENC... 365
e-100
gb|AC014977.1|AC014977 Drosophila melanogaster, \*** SEQUENC... 52
8e-06
A pseudogene ?
U4 -- two genes, both previously published.
gb|AC017832.1|AC017832 Drosophila melanogaster, \*** SEQUENC... 297
6e-80
my 010; U4-1. There are also two U2 genes and two U5 genes in this
contig.
gb|AC014745.1|AC014745 Drosophila melanogaster, \*** SEQUENC... 238
5e-62
my 011; U4-2
U5 -- 4 genes and 3 variant genes
gb|AC019603.1|AC019603 Drosophila melanogaster, \*** SEQUENC... 143
2e-33
This matches the published U5 RNA sequence for Drosophila U5. My
number 017.
gb|AC019965.1|AC019965 Drosophila melanogaster, \*** SEQUENC... 141
7e-33
This differs from the published U5 RNA in the 3' end stem-loop.
My number 017.
gb|AC019905.1|AC019905 Drosophila melanogaster, \*** SEQUENC... 139
3e-32
This differs from the published U5 RNA in the 3' end stem-loop.
My number 018.
gb|AC017727.1|AC017727 Drosophila melanogaster, \*** SEQUENC... 139
3e-32
This differs from the published U5 RNA in the 3' end stem-loop.
My number 019.
gb|AC019732.1|AC019732 Drosophila melanogaster, \*** SEQUENC... 137
1e-31
This differs greatly from the published U5 RNA in the 3' end
stem-loop.
My number 020.
gb|AC017832.1|AC017832 Drosophila melanogaster, \*** SEQUENC... 139
3e-32
These two genes differ greatly from the published U5 RNA in the 3'
end stem-loop.
My 021 and 022. There are also two U2 genes and a U4 gene in this
contig.
U6 -- 3 genes on a single contig. These were all previously described.
gb|AC018038.1|AC018038 Drosophila melanogaster, \*** SEQUENC... 212
2e-54
U11 -- MISSING! There is nothing in the genome that convincingly matches
U11. However, given the difficulty of finding highly divergent snRNAs,
this result is inconclusive. I tried hard, varying parameters and checking
all sites that match the snRNA promoter consensus, but I did not find any
convincing hits.
U12 -- 1 gene.
gb|AC014181.1|AC014181
nucleotides 16743-16506 (238 nt.).
U6atac -- 1 gene.
gb|AC018217.1|AC018217 Drosophila melanogaster, \*** SEQUENC... 74
1e-12
U4atac -- 1 gene
gb|AC013956.1|AC013956 Drosophila melanogaster, \*** SEQUENC... 52
5e-06
\##################################################
On Mon, 28 Feb 2000, Skupski, Marian P. wrote:
> Steve
>
> The sequences will be good enough. We're spending the next week or so
> getting the data ready to go to GenBank, and I can blast the sequences
and
> get coordinates ready if I have the sequences. I'll try to get the two
> extra U2 sequences added to the count that you sent to Mark.
>
> marian
\##################################################
Stephen M. Mount
Cell Biology and Molecular Genetics
H. J. Patterson Hall
University of Maryland
College Park, MD 20742-5815
Phone 301-405-6934
FAX 301-314-9081
permanent email address sm193@XXXX
\##################################################
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From smount@XXXX Fri Apr 28 04:08:17 2000
Envelope-to: ma11@XXXX
Delivery-date: Fri, 28 Apr 2000 04:08:17 +0100
X-Authentication-Warning: rac9.wam.umd.edu: smount owned process doing -bs
Date: Thu, 27 Apr 2000 23:13:05 -0400 (EDT)
From: Stephen M Mount <smount@XXXX>
To: Michael Ashburner <ma11@XXXX>
cc: flybase-helpXXXX, Helen Salz <hksXXXX>
Subject: snRNA report.
MIME-Version: 1.0
Content-Type: MULTIPART/MIXED; BOUNDARY='-559023410-851401618- 956891585=:3153 '
Content-Length: 21169
Michael,
You suggested that I send you a report of snRNA positions. Here it is!
I have not renamed ANYTHING. New genes have been named according to the
system used for the old names. Notes relevant to this are at the bottom,
below my assignments and above the reference RNA sequences.
It is interesting that there are three or four clusters of snRNA genes:
AE003639 at 34A -- three U2 genes and one U5 gene in 35 kb.
AE03664 at 38AB -- two U2, one U4, and two U5 genes in 6 kb.!!!
AE003501 at 14B -- a U2 gene and a U5 gene in 1 kb.
AE003604 and AE003603 at 82E -- two U1 genes and a U4atac gene some
unknown distance apart in beta heterochromatin.
\##################################################
On Sun, 2 Apr 2000, Michael Ashburner wrote:
> Steve
>
> All the tRNAs are are in the xml, since they are displayed on Genescene.
> Suzi might be able to provide a list with coordinates and (predicted)
> cytology.
>
> We might be able to give you some help in correlating existing snRNA
> genes with the Celera sequence. Aubrey can, I am sure, translate coordinates into
> approximate cytology and that might help.
>
> I would like to avoid, if at all possible, the naming of snRNA/tRNA genes from
> the Celera sequence independent of what FB has already.
>
> Michael
\##################################################
Gene name Promoter sequence and spacing to RNA Accession
RNA location
U1-21D taattcccaactgcttctggccatcagctcatggaaa 24 AE003588
18,650 18,813
U1-82Ea taattcccaactagttctagttgcgccctcatggaaa 24 X53542
2,592 2,755
U1-82Ec taattcccaactagttctagttgcgccctcatggaaa 24 AE003604
196,233 196,396
U1-95Ca caattcccaactggttttagctgctcagccatggaaa 24 AE003745
55,799 55,636
U1-95Cb taattcccaactggttctggctacttccctatggaga 24 AE003745
23,856 24,027
U1-95Cc aaattcccaaacagttctggcagatctctcaaggaga 24 AE003745
22,328 22,491
U2-14B taattcccaactggtcttggctgcagtcgcatcaagt 25 AE003501
221,890 222,081
U2-34ABa caattcccaactgcttctggccgtttgctcatggaga 25 AE003639
91,282 91,091
U2-34ABb gaattcccaactgcttctggccgtttggtcatggaga 25 AE003639
95,005 95,196
U2-34ABc taattcccaaatggttctggccgtttgcccatcgaga 25 AE003639
123,728 123,537
U2-38ABa taattcccaactgattttagctgcagtcgcatgaagt 25 AE003664
83,768 83,577
U2-38ABb taattctcaactgattttagctgcagtcgcatgaagt 25 AE003664
80,609 80,821
U4-38AB taattcccaaatggttctggcttgctgtgaatggaat 25 AE003664
78,697 78,838
U4-39B taattcccaactgcttctggcagcgccggcatggtat 25 AE003669
203,879 203,737
U4-25F taattctcaaaaggttttagcagactccgcatagaga 24 AE003610
126,856 127,003
U5-14B aaattcccaactccttctggccaacactgatcctaga 26 AE003501
221,335 221,226
U5-23D gaattcccaaaaagttctatcacagaacgaatctagg 25 AE003581
87,935 87,805
U5-34A tgattcccaacatgttcaagctcgttctaaatgatcg 25 AE003639
124,015 124,141
U5-35D tgattcccaacacgttcaagcaatttcttagtggtac 25 AE003648
179,845 179,720
U5-38ABa taattcccaagcggttctattcaatattgagtatgga 24 AE003664
80,037 79,911
U5-38ABb aaattcccaattccttctggccaatactgatcctaga 26 AE003664
84,377 84,503
U5-63BC taattcccaacgtgttaaagcagtcactgaatagagt 24 AE003477
26,662 27684
U6-96Aa tgattcccaagtacatattctgcaagagtacagtata 27 AE003748
102,469 102,574
U6-96Ab taattctcaactgctctttcctgatgttgatcattta 26 AE003748
103,072 103,178
U6-96Ac taattctcaacttctttttccagactcagttcgtata 26 AE003748
103,595 103,701
U4atac-82E taattcccaactagtactggccacttttgcttgaggt 21 AE003603
245,404 245,525
U6atac-29B aaattcccaagttctttttccgcatggagtgcttata 26 AE003621
31,949 32,045
U12-73B tgattcccaaccggttctggttgcatggccatgagtt 25 AE003526
210,776 210,539
Notes:
U1-82Ea is not in the Celera sequence. That could be due to a strain
difference or to an error in sequence assembly (the U1-82Ea and U1-82Ec
genes are located nearby and are nearly identical [Lo & Mount. Nucleic
Acids Res. 18: 6971-6979]). However, it should be noted that U1-82Ea
encodes the variant U1b which differs from U1a by a single nucleotide and
is known to be expressed in Kc cells and Oregon R flies. U1-82Eb is a
pseudogene and so is not listed. It lies between U1-82Ea and U1-82Ec and
is also missing from the Celera sequence. U1-95Cc encodes the U1c variant.
I have used the term U4d for U4-25F to avoid confusion. The U4a, U4b and
U4c sequences published by Guthrie and Patterson (A.R. Genetics 1988) are
attributed to Kiss, unpublished, and the U4-38AB gene resembles both U4a
and U4c (sometimes one and sometimes another) at points where they differ.
No U5 gene entirely agrees with the published RNA sequence. Distances to
the are cap site are therefore approximate.
------------------------------------
RNA sequences (for confirmation):
>gi|174317|gb|K00787.1|DROUR1A D. melanogaster U1 small nuclear RNA
GATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCGGTTCCTCCGGAGTGAGGCTTGGCCATTG
CACCTCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTCGTGCGTGTAATTTTTGGTAGCC
GGGAATGGCGTTCGCGCCGTCCCGA
>U2 snRNA (from various)
atcgcttctcggccttatggctaagatcaaagtgtagtatctgttcttatcagcttaacatctgatagttcctccattgg
aggacaacaaatgttaaactcatttttggaatcagacggagtgctaggggcttgctccacctctgtcacgggttggcccg
gtattgcagtaccgccgggatttcggcccaac
>gi|174319|gb|K03095.1|DROUR4 D. melanogaster U4 small nuclear RNA
AGCTTAGCGCAGTGGCAATACCGTAACCAATGAAGCCTCCCTGAGGTGCGGTTATTGCTAGTTGAAAACT
TTAACCAACCCACGCCATGGGACGTGAAATACCGTCCACTACGGCAATTTTTGGAAGCCCTTACGAGGGC
TAA
>gi|174320|gb|K03096.1|DROUR5 D. melanogaster U5 small nuclear RNA, 3' end
ATACTCTGGTTTCTCTTCAATGTCGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACA
CTCTAAGAGTCTAAAACTAATTTTTTAGTCAGTCTTGTCGCAAGACTGGGGCCA
>gi|8768|emb|X06669.1|DMU6 Drosophila melanogaster U6 snRNA
NGTTCTTGCTTCGGCAGAACATATACTAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCAGCGCA
AGGATGACACGCAAAATCGTGAAGCGTTCCACATTTTT
> Drosophila U4atac -- hypothetical
caataatgttataaataataaacaatttttaatttttagaaggaagtcaaaagtagagtgtaaatcgcttattacacttt
atttacaaacgatattttagtgtatgcaatatttcccttgc
> Drosophila U6atac -- hypothetical
gtgttgtttggaaggagagcaagttagcactcccctagacaaggatggaacacataaacggtcggctaggcacagacaaa
agccgtccacaaatttt
> Drosophila U12 -- hypothetical
gtgcctcaaactaatgagtaaggaaaaccaatcagccttgctaatcgcttggcagtattggcttctaggcaggggggcgt
gtcccgcgccccttgaagctcaaatttttgcaagggcacaggtcgtcccctcctcctccgcgtgggtggcgttcggccga
gcgaaccggcgcctactttgcgtccggctagcgaggatctctgggtgccatcccacggctgggtgttgcgatctgccc
\##################################################
Relevant text from Mount and Salz (manuscript in preparation for a special
issue of the Journal of Cell Biology):
The Drosophila genome contains multiple copies of the 5 UsnRNAs found in
the major class of sliceosomes. We found five genes for U1, six genes for
U2, three genes for U4, seven genes for U5, and three genes for U6. With
the exception of U4-25F, and the U5 genes (which were previously known
only by in situ hybridization), these genes had been described previously
[Lo, 1990; Saba, 1986; Das, 1987; Alonso, 1984; Saluz, 1988]. The variant
U4-25F gene presumably escaped detection because the predicted RNA has
only 69% identity with the major form of fly U4 [Saba, 1986] and 68% with
human U4. This degree of divergence is therefore quite high (human and fly
U4 share 73% identity), yet the gene is likely to be functional because
the promoter is conserved and some of the variation includes compensatory
changes that allow formation of the conserved stem loop structures.
The Drosophila genome also contains a minor class, or U12, introns [Hall,
1994; Tarn, 1996] and is therefore likely to contain the U12-type
spliceosome. Identification of snRNAs for the U12-type spliceosomes was
difficult because they had not been described previously, and were
somewhat diverged. However, by modification of the standard parameters for
blastn (see Methods), it was possible to find one gene for U12, one gene
for U6atac and one gene for U4atac. These are almost certainly real genes,
as critical sequences are conserved. In addition, the highly conserved
snRNA promoter, including a 9/10 or perfect match to the PSE consensus
TAATTCCCAA approximate 52 nucleotides upstream of the start [Lo, 1990 \#19;
Jensen, 1998] is present in each case. No U11 gene was found. This may be
due to divergence beyond what can be detected by blastn searches. However,
it is striking that the one identified protein component unique to the
U11/U12 snRNP (and minor spliceosome), the U11 35 kd. subunit [Will, 1999
\#20] cannot be found either. In fact, the U11 snRNP may not be required
for splicing, as its role should be 5' splice site recognition, and the
highly conserved minor splice site consensus is also complementary to
U6atac snRNA. Thus, minor class 5 splice sites could be recognized by the
U6atac snRNA alone, or by an unknown protein that acts during the early
steps of splicing. This mechanism would be analogous to a situation seen
in vitro where certain vertebrate introns can be processed in the absence
of U1 snRNP if the 5 splice sites can be recognized by U6 snRNA
[Crispino,1996 \#21].
\##################################################
Stephen M. Mount
Cell Biology and Molecular Genetics
H. J. Patterson Hall
University of Maryland
College Park, MD 20742-5815
Phone 301-405-6934
FAX 301-314-9081
permanent email address sm193@XXXX
\##################################################
From smount@XXXX Fri May 12 19:25:14 2000
Envelope-to: ma11@XXXX
Delivery-date: Fri, 12 May 2000 19:25:14 +0100
X-Authentication-Warning: rac3.wam.umd.edu: smount owned process doing -bs
Date: Fri, 12 May 2000 14:30:13 -0400 (EDT)
From: Stephen M Mount <smount@XXXX>
To: Michael Ashburner <ma11@XXXX>
Subject: Re: snRNA report - some questions
MIME-Version: 1.0
Michael,
Sorry to take so long to reply. I had meant to go back and check all of
the obscure Flybase snRNA entries (most of which are based on poor data),
but I haven't finished yet, and I am about to fly to CA for Gerry's 50th.
What follows is as far as I got.
Steve
\##################################################
> Steve .. I am now updating the snRNAs in FB with your data.
> I have some questions, which I need answered before I actually
> pass the updates on to the database.
>
> 0. You made some other minor changes
> to the names (ie the cytologies) .. were these on the basis of new evidence ?
>
> snRNA:U5:23DE > snRNA:U5:23D
> snRNA:U5:34AB > snRNA:U5:34A
> snRNA:U5:35EF > snRNA:U5:35D
> snRNA:U5:63A > snRNA:U5:63BC
The old evidence was in situ hybridization, and I suspect that some if it
was fairly inaccurate (see below). The names I assigned were based
entirely on the sequence. Specifically, on interpolation between nearby
genes within that same sequence accession (e.g. snRNA:U5:63BC is near
'BtbVII,' which was assigned to 63B-C). I recognize that this has it's own
problems. In this case, the BtbVII is over 50 kb. to the right, and the
only mapped gene on the adjacent accession, Shab, ='CG1066,' 63A1-63A7,'
is 130 kb. in the other direction.
> 1. snRNA:U2:39B. & snRNA:U2:40AB. FlyBase had these genes but with NO
> attached sequence. You have U2-38ABa and U2-38ABb. Do I assume one of
> them is the U2:39B gene & the other is the U2:40AB gene ?
Probably not. U2-38ABa and U2-38ABb are less than 3 kb. apart and would
not have been distinguished by the method used (in situ hybridization).
My response to the following questions is the same. The in situs in those
old papers were just not that good. Remember, snRNAs make short
probes. Your guess as to which is which is probably better than mine.
> 2. FB had these genes with these accession numbers. Not on your lists:
> snRNA:U2:84Ca , X04247
> snRNA:U2:84Cb , X04245, X04246
>
> 3. FB has snRNA:U4:39B , AQ034021 .. is this your U4:38AB
>
> 4. FB has snRNA:U4:40AB , no sequence .. is this your U4:39B
>
> 5. FB has U5:39B with no sequence data. Is this your U5:38ABa ?
>
> 6. FB has these:
> snRNA:U2:84Ca , X04247
> snRNA:U2:84Cb , X04245, X04246
>
> Not on your list
>
> 7. I think I asked you this before: Any idea what these are ?
>
> \*a snRNA-a
> \*z FBgn0003454
> \*x FBrf0042443 == Arrigo et al., 1985, EMBO J. 4: 399--406
> \*g M26817
> \#
> \*a snRNA-b
> \*z FBgn0003455
> \*x FBrf0042443 == Arrigo et al., 1985, EMBO J. 4: 399--406
> \*g M26818
> \#
> \*a snRNA-c
> \*z FBgn0003456
> \*x FBrf0042443 == Arrigo et al., 1985, EMBO J. 4: 399--406
> \*g M26819
> \#
> \*a snRNA-d
> \*z FBgn0003457
> \*x FBrf0042443 == Arrigo et al., 1985, EMBO J. 4: 399--406
> \*g M26820
> \#
> \*a snRNA:K2a
> \*z FBgn0016982
> \*x FBrf0038653 == gm626.h == Wooley et al., 1982, Proc. Natl. Acad. Sci. USA 79(22): 6762--6766
> \#
> \*a snRNA:K2b
> \*z FBgn0016981
> \*x FBrf0038653 == gm626.h == Wooley et al., 1982, Proc. Natl. Acad. Sci. USA 79(22): 6762--6766
> \#
> \*a snRNA:K8
> \*z FBgn0016980
> \*x FBrf0038653 == gm626.h == Wooley et al., 1982, Proc. Natl. Acad. Sci. USA 79(22): 6762--6766
> \#
> \*a snRNA:K9
> \*z FBgn0016979
> \*x FBrf0038653 == gm626.h == Wooley et al., 1982, Proc. Natl. Acad. Sci. USA 79(22): 6762--6766
> \#
>
> \*g is the sequence accession and \*x the reference
>
> Thanks for all the help.
>
> Michael
>
