Reference Report

Here are the matches of the nc2 class to CGs where possible, and to the
scaffolds, where there was not CG.
cheers,
sima> nc2: genes with no SWP but with either TREMBL or PIR (47). Quite a
> few of these have a PIR entry and no nucleic acid one -- no idea
> what that means. Again some of these (commented) have already been
> looked at.
> X-Sun-Data-Name: nc2
> Acp98AB - Cat 1 residue
=new exon in first intron of CG12879 CT32023 FBan0012879 FBgn0039540>gb|AE003762.1|AE003762 Drosophila melanogaster genomic scaffold
142000013386035 section 87 of
105, complete sequence
Length = 230995
Score = 52.3 bits (123), Expect = 2e-07
Identities = 24/26 (92%), Positives = 24/26 (92%)
Frame = +2
Query: 2 EFPNPVLSRIGRSLRTNKGTHYQRMT 27
E NPVLSRIGRSLRTNKGTHYQRMT
Sbjct: 33911 EVTNPVLSRIGRSLRTNKGTHYQRMT 33988
Database: Drosophila Genome
Posted date: Apr 10, 2000 4:44 PM
Number of letters in database: 122,680,987
Number of sequences in database: 1181> Acph-1
(438aa)
=CG7899|FBan0007899|CT6619|FBan0007899 last_updated:000321 (438aa)
95% id over 438aa> anon-63BC-T3
O18384(31aa) by BLASTP against predicted proteins at BDGP
=CG14965|FBan0014965|CT34811|FBan0014965 last_updated:000321(537aa)
Score = 65 (22.9 bits), Expect = 0.049, P = 0.048
Identities = 11/11 (100%), Positives = 11/11 (100%)
Query: 21 MHFFKFPVKDP 31
MHFFKFPVKDP
Sbjct: 1 MHFFKFPVKDP 11
missing first 20aa in CG> anon-67Ea - Cat 9 residue, BLASTN finds CGless seq
CAA48385(170aa) by BLASTP against predicted proteins at BDGP
=no protein in GadFly
GenBank:X68309(2578bp) by BLASTN against all at BDGP
=gb|AE003547|Drosophila melanogaster genomic scaffold, 142000013386050
section 34 of 54, complete sequence
very approximately (need sim4 alignment)
~1987-900 = 254926-256070, 163-865 = 256739-256036, 2568-1973 = 254288-254883,
164-68 = 256797-256893, 71-1 = 257060-257130
> Crlbp
S65395(11aa) by Pattern Search against predicted proteins at BDGP
=FBan0001668=CG1668|FBan0012467|CT4586=Pbprp2=FBgn0011280
> ect
A61047(280aa) by BLASTP against predicted proteins at BDGP
=CG11965|FBan0011965|CT37129|FBan0011965 last_updated:000321(429aa)
Score = 168 (59.1 bits), Expect = 5.1e-19, Sum P(2) = 5.1e-19
Identities = 38/50 (76%), Positives = 38/50 (76%)
Query: 1 MKFVIXXXXXXXXXXQIEASPLQRLSRSERAVSPQQTVNNEVAPAVRPAS 50
MKFVI QIEASPLQRLSRSERAVS QQTVNNEVAPAV PAS
Sbjct: 1 MKFVILLCVLSALLLQIEASPLQRLSRSERAVSRQQTVNNEVAPAVAPAS 50
Score = 75 (26.4 bits), Expect = 5.1e-19, Sum P(2) = 5.1e-19
Identities = 17/41 (41%), Positives = 17/41 (41%)
Query: 155 LDEXXXXXXXXXXXGISDGVDLPAESXXXXXXXXXXXXXDE 195
LDE GISDGVDLPAES DE
Sbjct: 155 LDEVAPAAASSVSAGISDGVDLPAESGNAAEVLAAGNAADE 195
> EG:34F3.2 - part of CG12467
O77432(504aa) by BLASTP against predicted proteins at BDGP
=CG12467|FBan0012467|CT32681|FBan0012467 last_updated:000321(1376aa)
77-524 of CG12467 corresponds to 38-485 of EG:34F3.2
40-47 of ' 1-8 '> Gprk3
C41615(55aa) by BLASTP against predicted proteins at BDGP
=CG8224|FBan0008224|CT8241|FBan0008224 last_updated:000321(601aa)
Score = 268 (94.3 bits), Expect = 8.0e-24, P = 8.0e-24
Identities = 51/55 (92%), Positives = 54/55 (98%)
Query: 1 VVYRDLKSKNILVKSNLSCAIGDLGLAVRHVEKNDSVDIPSTHRVGTKRYMAPEI 55
+ +RDLKSKNILVKSNLSCAIGDLGLAVRHVEKNDSVDIPSTHRVGTKRYMAPE+
Sbjct: 427 IAHRDLKSKNILVKSNLSCAIGDLGLAVRHVEKNDSVDIPSTHRVGTKRYMAPEV 481> Gprk4
D41615(49aa) by BLASTP against predicted proteins at BDGP
=CG3051|FBan0003051|CT10258|FBan0003051 last_updated:000321(582aa)
Score = 222 (78.1 bits), Expect = 7.1e-19, P = 7.1e-19
Identities = 43/50 (86%), Positives = 46/50 (92%)
Query: 1 VVYRDLKPKNLLLDHNMHAKIADFGLSNMMLDGEFLRTSA-SPNYMAPEV 49
+V+RDLKP+NLLLDHNMH KIADFGLSNMMLDGEFLRTS SPNY APEV
Sbjct: 147 IVHRDLKPENLLLDHNMHVKIADFGLSNMMLDGEFLRTSCGSPNYAAPEV 196> GstD21
D46681(214aa) by BLASTP against predicted proteins at BDGP
=CG4181|FBan0004181|CT13804|FBan0004181 last_updated:000321(215aa)
214/214 (100%) id> GstD23
E46681(214aa) by BLASTP against predicted proteins at BDGP
=CG11512|FBan0011512|CT36385|FBan0011512 last_updated:000321(215aa)
213/214 (99%) id> GstD24
C46681(215aa) by BLASTP against predicted proteins at BDGP
=CG12242|FBan0012242|CT13898|FBan0012242 last_updated:000321(210aa)
209/215 (97%) id (gap of 6aa in subject)> GstD25
B46681(214aa) by BLASTP against predicted proteins at BDGP
=CG4423|FBan0004423|CT13946|FBan0004423 last_updated:000321(215aa)
214/214 (100%) id> GstD26
H46681(170aa) by BLASTP against predicted proteins at BDGP
=CG4371|FBan0004371|CT13952|FBan0004371 last_updated:000321(224aa)
170/170 (100%) id> GstD27
JQ1378(212aa) by BLASTP against predicted proteins at BDGP
=CG4421|FBan0004421|CT13954|FBan0004421 last_updated:000321(212aa)
211/212 (99%) id> Gta
D46036(150aa) by BLASTP against predicted proteins at BDGP
=CG4268|FBan0004268|CT13850|FBan0004268 last_updated:000321(952aa)
Score = 705 (248.2 bits), Expect = 5.5e-71, P = 5.5e-71
Identities = 147/152 (96%), Positives = 147/152 (96%)
Query: 1 VVYRAKDKRTNEIEALKRLKMEKEKEGFPITSRREINTLLKGGQHPNIVTVREIVVGSNM
60
VVYRAKDKRTNEI ALKRLKMEKEKEGFPITS REINTLLKG QHPNIVTVREIVVGSNM
Sbjct: 571 VVYRAKDKRTNEIVALKRLKMEKEKEGFPITSLREINTLLKG-QHPNIVTVREIVVGSNM
629
Query: 61 DKIFIVMDYVEHDLKSLMETMKNRKQSFFPGEVKCLTQQL-RAVAHLHDN-ILHRDLKTS
118
DKIFIVMDYVEHDLKSLMETMKNRKQSFFPGEVKCLTQQL RAVAHLHDN ILHRDLKTS
Sbjct: 630 DKIFIVMDYVEHDLKSLMETMKNRKQSFFPGEVKCLTQQLLRAVAHLHDNWILHRDLKTS
689
Query: 119 NLLLSHKGILKVGDFGLAREYGSPIKK-TSLVV 150
NLLLSHKGILKVGDFGLAREYGSPIKK TSLVV
Sbjct: 690 NLLLSHKGILKVGDFGLAREYGSPIKKYTSLVV 722> Hmx
Q24016(34aa) by BLASTP against predicted proteins at BDGP
=CG5832|FBan0005832|CT18293|FBan0005832 last_updated:000321(263aa)
Score = 169 (59.5 bits), Expect = 3.5e-14, P = 3.5e-14
Identities = 34/34 (100%), Positives = 34/34 (100%)
Query: 1 FDLKRYLSSSERAGLAASLRLTETQVKIWFQNRR 34
FDLKRYLSSSERAGLAASLRLTETQVKIWFQNRR
Sbjct: 158 FDLKRYLSSSERAGLAASLRLTETQVKIWFQNRR 191> Hrb85CD - probably same gene as Hrb87F
Q24486(386aa) by BLASTP against predicted proteins at BDGP
=CG12749|FBan0012749|CT27250|FBan0012749 last_updated:000321(385aa)
198/198 (100%) id> ImpE3
A61046(331aa) by BLASTP against predicted proteins at BDGP
=CG2723|FBan0002723|CT9257|FBan0002723 last_updated:000321(325aa)
188/191 (98%) id> l(2)rot - Cat 2 residue, BLASTN finds CGless seq
S42089(542aa) by BLASTP against predicted proteins at BDGP
=no proteins in GadFly
X95246(2818bp) by BLASTN against all at BDGP
=overlaps on opposite strand CG5504
CG5504|FBan0005504|CT17450|FBan0005504 last_updated:000321(1635bp)
very approximately (need sim4 alignment)
~2632-1240, 1100-843 = 1-1365, 1378-1635bp of CG
=gadfly|SEG:AE003461|gb|AE003461|Drosophila melanogaster genomic scaffold
142000013386038 section 10 of 15, complete sequence.
2818-1 = 228045-230862 of scaffold> l(3)73Ah
PIR:JC4296(222aa) by BLASTP against predicted proteins at BDGP
=CG4195|FBan0004195|CT13794|FBan0004195 last_updated:000321(222aa)
221/222 (99%) id> Lcp6 - Cat 1 residue, BLASTN finds CGless seq
SPTREMBL:P92184(104aa) by BLASTP against predicted proteins at BDGP
=no proteins in GadFly
U84756(473bp) by BLASTN against all at BDGP
=gb|AE003563|Drosophila melanogaster genomic scaffold 142000013386050
section 50 of 54, complete sequence.
very approximately (need sim4 alignment)
330-13 = 242870-243193, poor but 462-334 = 27439-27567> Lcp65Ab1 - Cat 2 residue, BLASTN finds CGless seq
SPTREMBL:P92192(104aa) by BLASTP against predicted proteins at BDGP
=no proteins in GadFly
U84747(947bp) by BLASTN against all at BDGP
=gb|AE003563|Drosophila melanogaster genomic scaffold 142000013386050
section 50 of 54, complete sequence.
very approximately (need sim4 alignment)
946-1 = 242514-243462> Lcp65Ab2 - Cat 2 residue, BLASTN finds CGless seq
SPTREMBL:P92192(104aa) by BLASTP against predicted proteins at BDGP
=no proteins in GadFly
U84746(855bp) by BLASTN against all at BDGP
=gb|AE003563|Drosophila melanogaster genomic scaffold 142000013386050
section 50 of 54, complete sequence.
very approximately (need sim4 alignment)
855-1 = 245477-246316> Mat89Ba
SPTREMBL:Q27924(545aa) by BLASTP against predicted proteins at BDGP
=CG6814|FBan0006814|CT21143|FBan0006814 last_updated:000321(689aa)
CG has extra 27aa at N-term, a few polymorphisms> Mst40 - possibly untranslated? (Aubrey Apr 4)
SPTREMBL:Q24437(23aa) by BLASTP against predicted proteins at BDGP
=no proteins in GadFly
Z22588(1387bp) by BLASTN against all at BDGP
=gb|AE003466|Drosophila melanogaster genomic scaffold 142000013386038
section 15 of 15, complete sequence.
very approximately (need sim4 alignment)
1-1387 = 161926-163314
1-799 = 163309-164114, ~800-1387 = 164130-164722
(two closely related genes near each other)> NaCP37B - Cat 1 residue
SPTREMBL:Q24308(113aa) by BLASTP against predicted proteins at BDGP
=no proteins in GadFly
X84408(384bp) by BLASTN against all at BDGP
=CG9071|FBan0009071|CT24831|FBan0009071 last_updated:000321(7375bp)
very approximately (need sim4 alignment)
1-240 = 6438-6677 of CG, 241-377 = 6700-6823 of CG
> ph-d
PIR:S23632(1589aa) by BLASTP against predicted proteins at BDGP
=CG3895|FBan0003895|CT12875|FBan0003895 last_updated:000321(1211aa)
from 130-594 of CG3895, CG missing exon, then a few other polymorphisms
till end of CG, then
=CG18414|FBan0018414|CT41888|FBan0018414 last_updated:000321(290aa)
from 1300 to 1589 of S23632 for all of CG> Pk1
SPTREMBL:Q24057(36aa) by BLASTP against predicted proteins at BDGP
=no proteins in GadFly
U23827(110bp) by BLASTN against all at BDGP
=gb|AE002760|Drosophila melanogaster genomic scaffold 142000013386034, complete sequence.
1-110 = 24362-24471>PpD19
SPTREMBL:Q26247(24aa) by BLASTP against predicted proteins at BDGP
=CG10930|FBan0010930|CT30615|FBan0010930 last_updated:000321(314aa)
24/24 (100%) id> PpD3
PIR:AAB22463(25aa) by BLASTP against predicted proteins at BDGP
=CG8402|FBan0008402|CT24679|FBan0008402 last_updated:000321
25/25 (100%) id> PpD33
PIR:AAB22469(24aa) by BLASTP against predicted proteins at BDGP
=CG9842|FBan0009842|CT27780|FBan0009842 last_updated:000321(570aa)
24/24 (100%) id> PpD5
PIR:AAB22464(24aa) by BLASTP against predicted proteins at BDGP
=CG10138|FBan0010138|CT10817|FBan0010138 last_updated:000321(346aa)
24/24 (100%) id> PpD6
PIR:AAB22465 (24aa) by BLASTP against predicted proteins at BDGP
=CG8822|FBan0008822|CT25390|FBan0008822 last_updated:000321(336aa)
24/24 (100%) id>prd3
PIR:AAA28839(38aa) by BLASTP against predicted proteins at BDGP
=no protein in GadFly
M14551(114bp) by BLASTN against all at BDGP
=CG10037|FBan0010037|CT28091|FBan0010037 last_updated:000321(2556bp)
1-114 = 2122-2235> Rbp10
PIR:I48110(44aa) by BLASTP against predicted proteins at BDGP
=CG3151|FBan0003151|CT38165|FBan0003151 last_updated:000321(68aa)
=CG3151|FBan0003151|CT10570|FBan0003151 last_updated:000321(673aa)
43/43 (100%) id, 114-156 of CG
> Rbp11
PIR:A47752(39aa) by BLASTP against predicted proteins at BDGP
=no protein in GadFly
closest match:
CG17136|FBan0017136|CT38058|FBan0017136 last_updated:000321
Length = 135
Score = 152 (53.5 bits), Expect = 2.2e-12, P = 2.2e-12
Identities = 29/39 (74%), Positives = 30/39 (76%)
Query: 1 FVGNLAPRRSKPRDRSAFAKYGPLRNVWVARNPPGFAFV 39
+VGNL SK AFAKYGPLRNVWVARNPPGFAFV
Sbjct: 14 YVGNLGSSASKHEIEGAFAKYGPLRNVWVARNPPGFAFV 52
S51740(117bp) by BLASTN agianst all at BDGP
=CG17136|FBan0017136|CT38058|FBan0017136 last_updated:000321(511bp)
Plus Strand HSPs:
Score = 490 (73.5 bits), Expect = 2.3e-16, P = 2.3e-16
Identities = 110/117 (94%), Positives = 110/117 (94%), Strand = Plus / Plus
Query: 1 TTCGTGGGGAACCTGG-CTCCTCGGCGCTCCAAGCCACGAGATAGAAG-CGCATTTGCCA 58
T CGTGGG AACCTGG CTCCTCGGCG TCCAAGC ACGAGATAGAAG CGCATTTGCCA
Sbjct: 93 TACGTGGGAAACCTGGGCTCCTCGGCG-TCCAAGC-ACGAGATAGAAGGCGCATTTGCCA 150
Query: 59 AATATGGACCCCTGCGAAACGTGTGGGTGGCCCGCAATCCACCAGGGTTCGCTTTCGTC 117
AATATGGACCCCTGCGAAACGTGTGGGTGGCCCGCAATCCACCAGG TTCGC TT GTC
Sbjct: 151 AATATGGACCCCTGCGAAACGTGTGGGTGGCCCGCAATCCACCAGGTTTCGCCTTTGTC 209> Rbp12
PIR:B47752(41aa) by BLASTP against predicted proteins at BDGP
=CG5422|FBan0005422|CT17178|FBan0005422 last_updated:000321(464aa)
=CG5422|FBan0005422|CT17194|FBan0005422 last_updated:000321(464aa)
39/41 (95%) id
> Rbp2
PIR:B48110(43aa) by BLASTP against predicted proteins at BDGP
=CG4429|FBan0004429|CT14414|FBan0004429 last_updated:000321(325aa)
40/43 (93%) id, 32-74 of CG> Rbp3
PIR:C48110(44aa) by BLASTP against predicted proteins at BDGP
=CG17791|FBan0017791|CT39414|FBan0017791 last_updated:000321(378aa)
31/32 (96%) id, 149-180 of CG> Rbp5
PIR:E48110(48aa) by BLASTP against predicted proteins at BDGP
=no protein in GadFly
S51706(144bp) by BLASTN against all at BDGP
overlaps opposite strand of
CG3373|FBan0003373|CT11347|FBan0003373 last_updated:000321(2291bp)
Minus Strand HSPs:
Score = 635 (95.3 bits), Expect = 2.6e-22, P = 2.6e-22
Identities = 135/141 (95%), Positives = 135/141 (95%), Strand = Minus / Plus
Query: 143 ACGAAACCGAA-CCCACTACCAAGACGACAACTACTACAACCACGCCAAAGCCCACTACC 85
AC A CCGAA CCCACTACCAAGACGACAACTACTACAACCACGCCAAAGCCCACTACC
Sbjct: 1470 ACCACGCCGAAACCCACTACCAAGACGACAACTACTACAACCACGCCAAAGCCCACTACC 1529
Query: 84 ACAACGACAACCAAGAAGCCAACGACCACTACCACCACTACGACAACCACGCCGAAGCCA 25
ACAACGACAACCAAGAAGCCAACGACCACTACCACCACTACGACAACCACGCCGAAGCCA
Sbjct: 1530 ACAACGACAACCAAGAAGCCAACGACCACTACCACCACTACGACAACCACGCCGAAGCCA 1589
Query: 24 ACAACTACTTAGTCCGCCAACA 3
ACAACTACT AG CCGCC ACA
Sbjct: 1590 ACAACTACTAAG-CCGCCGACA 1610> Rbp6
PIR:F48110(44aa) by BLASTP against predicted proteins at BDGP
=no protein in GadFly
S51715(132bp) by BLASTN against all at BDGP
=gb|AE003524|Drosophila melanogaster genomic scaffold 142000013386050 section
11 of 54, complete sequence.
Plus Strand HSPs:
Score = 430 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
Identities = 90/95 (94%), Positives = 90/95 (94%), Strand = Plus / Plus
Query: 30 TCCAGAGAGCTTACGCGATTACTTCGGACGTTACGGTGATATCTCAGAGGCTATGGTCAT 89
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 314913 TTCAGAGAGCTTACGCGATTACTTCGGACGTTACGGTGATATCTCAGAGGCTATGGTCAT 314972
Query: 90 GAAGGATCCCACGACGCGCAGATCCAGAGGTTTTG 124
||||||||||||||||||||||||||| | |||
Sbjct: 314973 GAAGGATCCCACGACGCGCAGATCCAGGTGAGTTG 315007
> Rbp7
PIR:G48110(44aa) by BLASTP against predicted proteins at BDGP
=CG10377|FBan0010377|CT29098|FBan0010377 last_updated:000321(421aa)
44/44 (100%) id, 10-53 of CG> Rbp8
PIR:H48110(36aa) by BLASTP against predicted proteins at BDGP
=CG10851|FBan0010851|CT41998|FBan0010851 last_updated:000321(132aa)
=CG10851|FBan0010851|CT30371|FBan0010851 last_updated:000321(329aa)
31/36 (86%) id> repo - part of CG8045
PIR:A54282(612aa) by BLASTP against predicted proteins at BDGP
=CG8045|FBan0008045|CT24072|FBan0008045 last_updated:000321(612aa)
> Rya-r76CD - misassigned to CG10844
PIR:B49131(508aa) by BLASTP against predicted proteins at BDGP
=CG10844|FBan0010844|CT30357|FBan0010844 last_updated:000321(5107aa)
C terminal 4599-5107aa of CG
Z18536(1528bp) by BLASTN against all at BDGP
=CG10844|FBan0010844|CT30357|FBan0010844 last_updated:000321(15606bp)
1-1528 = 13794-15325