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