Reference Report

From leyla@XXXXXXXXXXXXXXX Thu Nov 02 01:19:12 2000
Envelope-to: ag24@XXXXXXXXXXXXXXX
Delivery-date: Thu, 2 Nov 2000 01:19:12 +0000
Date: Wed, 1 Nov 2000 20:18:24 -0500 (EST)
From: Leyla Bayraktaroglu <leyla@XXXXXXXXXXXXXXX>
Reply-To: Leyla Bayraktaroglu <leyla@XXXXXXXXXXXXXXX>
Subject: Current list of possibly CG-able known genes
To: ag24@XXXXXXXXXXXXXXX
Cc: curatorsXXXXXXXXXXXXXXX, joelXXXXXXXXXXXXXXX
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Hi Aubrey,
Attached are the CG-to-known gene correspondences for some
of the genes in the nc4 and nc6 categories.
nc4: genes with no SWP/TREMBL/PIR entry or protein_id but which look
like ESTs (428).
nc6: everything else with a nucleic acid entry (115).
Joe Lemaire did batch BLAST of accessions attached to the gene
against predicted transcripts (CTs) and Celera/BDGP scaffolds,
and I scanned the output. Additional alignments were performed
as necessary.
Also ttached are the few genes that I have been able to
resolve from the nc7 file.
nc7: genes with no nucleic acid or protein accessions but which still
feature in 'gene order' statements in the genes data (548).
These fall into 2 categories:
1.sequence data was in paper but not in the sequence databanks
(very straightforward) (nc7_done)
2. there was detailed molecular information that made it
easy to place the genes. These are marked with 'curator inference'
(nc7_inference).
anon-EST:CL1c2 RhoL (CG9366|FBan0009366|CT26615|)
anon-EST:CL2c12 Act57B (CG10067|FBan0010067|CT28343|)
anon-EST:CL2d4 CG4677|FBan0004677|CT15069|
anon-EST:CL32 CadN (CG7100|FBan0007100|CT21941|) 3'UTR
anon-EST:CL57 CG-less at AE003457:118582..118646,118706..118748
between CG6044 and qkr58E-3
anon-EST:fe1A1 mt:lrRNA
Query= gi|2130664|gb|AA433202.1|AA433202 EST1 Drosophila
melanogaster Uni-ZAP XR library (Stratagene cat.#937602) Drosophila
melanogaster cDNA clone 1A1 5'.
(190 letters)>emb|X53506.1|DM16SR Drosophila mRNA to mitochondrial 16S ribosomal RNA gene
Length = 1324
Score = 232 bits (117), Expect = 4e-59
Identities = 155/164 (94%), Gaps = 3/164 (1%)
anon-EST:fe1A11 CG-less at AE003558:101280..101518
anon-EST:fe1A12 aligns to several scaffolds: repeat?
anon-EST:fe1A2 CG7808|FBan0007808|CT5020|
anon-EST:fe1A5 CG1475|FBan0001475|CT2508| (anon-EST:Posey125)
anon-EST:fe1A7 CG7971|FBan0007971|CT6255|
transcript structure to be fixed
_______________________________________________________________________________
anon-EST:fe1B1 mt:Cyt-b
BLAST of AA433193 against AF200828
Score = 360 bits (187), Expect = 5e-98
Identities = 245/262 (93%), Positives = 245/262 (93%), Gaps = 8/262 (3%)
Query: 1 agctccaattaatatt--aagatnnnngaaattttngatcattacttggattatgtttaa 58
|||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||
Sbjct: 10557 agctccaattaatatttcaagatgat-gaaattttggatcattacttggattatgtttaa 10615
cytochrome b 24 A P I N I S S W W N F G S L L G L C L
Query: 59 ttattcaaattttaaccggattatttttagctatacattacacagctgatattaatctag 118
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10616 ttattcaaattttaaccggattatttttagctatacattacacagctgatattaatctag 10675
cytochrome b 43 I I Q I L T G L F L A M H Y T A D I N L
Query: 119 ctttctatagtgttaatcatatttgtcgaaacgttaattatggttgattattacgaactt 178
||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct: 10676 ctttctatagtgttaatcatatttgtcgagacgttaattatggttgattattacgaactt 10735
cytochrome b 63 A F Y S V N H I C R D V N Y G W L L R T
Query: 179 tatatgctaa-ggtgcatca--ttttcnnatttgtatttacttacatgtaggacgagg-a 234
|| ||||||| ||||||||| |||| ||||||||||||||||||||||||||||| |
Sbjct: 10736 tacatgctaacggtgcatcatttttttttatttgtatttacttacatgtaggacgaggaa 10795
cytochrome b 83 L H A N G A S F F F I C I Y L H V G R G
Query: 235 tttattacgg-tcatataaatt 255
|||||||||| |||||||||||
Sbjct: 10796 tttattacggttcatataaatt 10817
cytochrome b 103 I Y Y G S Y K F
_______________________________________________________________________
anon-EST:fe1B12 dpn (CG8704|FBan0008704|CT3681|)
anon-EST:fe1B5 CG-less at AE003622:192526..192731
anon-EST:fe1B9 matches CG-less at AE003502:117020..117354
anon-EST:fe1C10 CG9354|FBan0009354|CT25494|
anon-EST:fe1C12 CG4111|FBan0004111|CT13646|
anon-EST:fe1C6 matches CG-les at AE003578:233366..233808
anon-EST:fe1D1 RpL13 (CG4651|FBan0004651|CT15029|)
anon-EST:fe1D11 CG8589|FBan0008589|CT24993|
anon-EST:fe1D11 CG8589|FBan0008589|CT24993|
anon-EST:fe1D2 CG8857|FBan0008857|CT25442|
anon-EST:fe1D4 CG10652|FBan0010652|CT29824|
anon-EST:fe1E12 CG16912|FBan0016912|CT10134|
anon-EST:fe1E4 CG-less at AE003790:179593..179374,171576..171357
anon-EST:fe1E6 CG3329|FBan0003329|CT10524|
anon-EST:fe1E8 CG9354|FBan0009354|CT25494|
anon-EST:fe1F11 CG-less at AE003455:29428..29123
anon-EST:fe1G6 CG3329|FBan0003329|CT10524|
anon-EST:fe1G7 mbt (CG18582|FBan0018582|CT14490|)
(AA433228 aligned to mbt)
alignment with mbt acc. AJ011578 extends 3' end of
last exon of mbt on AE003502 to 279638
anon-EST:fe1H3 CG8933|FBan0008933|CT25652|CT41767
anon-EST:fe1H6 CG5802|FBan0005802|CT18200|
anon-EST:fe2A1 CG5820|FBan0005820|CT18251|
anon-EST:fe2A11 CG6605|FBan0006605|CT20532|
anon-EST:fe2A3 CG10305|FBan0010305|CT28945|
MERGE:
anon-EST:fe2A9 CG17467|FBan0017467|CT38621| (AA433262 aligned to AA433242)
anon-EST:fe2E7 CG17467|FBan0017467|CT38621|
anon-EST:fe2B1 trn (CG11280|FBan0011280|CT31487|)
anon-EST:fe2B11 CG-less at AE003767:46459..46126
anon-EST:fe2B3 CG-less at AE003484:50065..49882
anon-EST:fe2B6 CG3800|FBan0003800|CT12687|
anon-EST:fe2D1 RpL23a (CG7977|FBan0007977|CT6274|)
MERGE:
anon-EST:fe2D10 CG3773|FBan0003773|CT12578| (AA433250 aligned to AE003725)
anon-EST:fe2D12 CG3773|FBan0003773|CT12578| (AA433251 aligned to AA433250)
anon-EST:fe2D3 RpS18 (CG8900|FBan0008900|CT25560|)
anon-EST:fe2E12 Trl (CG9343|FBan0009343|CT40931| CT26545|)
anon-EST:fe2E2 alpha-Spec (CG1977|FBan0001977|CT6173|)
anon-EST:fe2E3 CG10712|FBan0010712|CT30015|
anon-EST:fe2E5 CG16803|FBan0016803|CT40743||CT34211|
anon-EST:fe2E7 CG17467|FBan0017467|CT38621|
anon-EST:fe2G4 CG1935|FBan0001935|CT5993|
anon-EST:fe2H10 CG3186|FBan0003186|CT10685|
anon-EST:fe2H6 CG7839|FBan0007839|CT23793|
anon-EST:fe2H7 sina (CG9949|FBan0009949|CT28005|)
anon-EST:fe3A1 CG2249|FBan0002249|CT7468|
anon-EST:fe3A6 RpL9 (CG6141|FBan0006141|CT37413|)
anon-EST:fe3B12 CG12859|FBan0012859|CT31999|
anon-EST:fe3B4 CG8495|FBan0008495|CT24837|
anon-EST:fe3C6 CG9177|FBan0009177|CT26238|CT41796
anon-EST:fe3C7 CG7088|FBan0007088|CT21889|
anon-EST:fe3C9 Khc-73 (CG8183|FBan0008183|CT21931|)
anon-EST:fe3D10 Ance (CG8827|FBan0008827|CT25364|)
anon-EST:fe3D3 CG5738|FBan0005738|CT18040|
anon-EST:fe3D7 Crc (CG9429|FBan0009429|CT26738|)
anon-EST:fe3D9 CG8983|FBan0008983|CT25820|
anon-EST:Liang-1.1 SsRbeta (CG5474|FBan0005474|CT17318|)
anon-EST:Liang-2.38 CG6876|FBan0006876|CT21288|
anon-EST:Liang-2.44 CG17836|FBan0017836|CT39616|
anon-EST:Liang-2.45 CG7546|FBan0007546|CT15742|
anon-EST:ParkEST009 CG8399|FBan0008399|CT18617|
anon-EST:ParkEST060 CG7532|FBan0007532|CT23067|
anon-EST:ParkEST066 CG7714|FBan0007714|CT21023|
anon-EST:ParkEST107 CG2297|FBan0002297|CT7648|
anon-EST:ParkEST130 CG9496|FBan0009496|CT26888|
anon-EST:ParkEST153 CG9675|FBan0009675|CT27358|
anon-EST:ParkEST161 graal (CG4948|FBan0004948|CT15880|)
anon-EST:ParkEST167 CG7658|FBan0007658|CT23381|
anon-EST:ParkEST180 Gasp (CG10287|FBan0010287|CT28895|)
anon-EST:ParkEST188 CG7013|FBan0007013|CT21690|
anon-EST:ParkEST240 CG7663|FBan0007663|CT23427|
anon-EST:ParkEST264 Fer2LCH (CG1469|FBan0001469|CT3604|)
anon-EST:ParkEST270 Sap-r (CG12070|FBan0012070|CT4748|)
anon-EST:ParkEST360 CG7348|FBan0007348|CT22655|
anon-EST:ParkEST398 CG7298|FBan0007298|CT22503|
anon-EST:Posey10 CG6105|FBan0006105|CT19171|
anon-EST:Posey100 CG11771|FBan0011771|CT33040|
anon-EST:Posey103 CG6514|FBan0006514|CT20253|
anon-EST:Posey104 CG5644|FBan0005644|CT16909|
anon-EST:Posey105 CG12194|FBan0012194|CT10091|
anon-EST:Posey109 CG13929|FBan0013929|CT33468|
anon-EST:Posey113 CG10802|FBan0010802|CT10681|
anon-EST:Posey114 CG13094|FBan0013094|CT32319|
anon-EST:Posey116 CG2789|FBan0002789|CT9517|
anon-EST:Posey12 CG7224|FBan0007224|CT22279|
anon-EST:Posey120 CG10157|FBan0010157|CT28567|
anon-EST:Posey121 Med (CG1775|FBan0001775|CT5334|)
anon-EST:Posey125 CG1475|FBan0001475|CT2504|
anon-EST:Posey127 CG15697|FBan0015697|CT35898|
anon-EST:Posey132 CG4721|FBan0004721|CT15195|
anon-EST:Posey135 CG9374|FBan0009374|CT26569|
MERGE
anon-EST:Posey137 CG8332|FBan0008332|CT24587|
anon-EST:Posey185 CG8332|FBan0008332|CT24587|
anon-EST:Posey14 scf (CG9148|FBan0009148|CT1311|)
MERGE
anon-EST:Posey140 CG8395|FBan0008395|CT18601|
anon-EST:Posey187 CG8395|FBan0008395|CT18601|
anon-EST:Posey141 CG4769|FBan0004769|CT15355|
anon-EST:Posey143 CG11015|FBan0011015|CT30186|
anon-EST:Posey148 EG:114D9.1 (CG11408|FBan0011408|CT31847|)
anon-EST:Posey150 Cyp9f2 (CG11466|FBan0011466|)
anon-EST:Posey151 MERGE with noe, no CG annotated
anon-EST:Posey153 CG7630|FBan0007630|CT23291|
anon-EST:Posey157 CG4111|FBan0004111|CT13646|
anon-EST:Posey158 CG8415|FBan0008415|CT24703|
anon-EST:Posey160 CG7646|FBan0007646|CT23353|
anon-EST:Posey161 CG8369|FBan0008369|CT24651|
anon-EST:Posey162 CG6549|FBan0006549|CT20403|
anon-EST:Posey167 CG3560|FBan0003560|CT11966|CT13660|
anon-EST:Posey169 CG9890|FBan0009890|CT27874|
anon-EST:Posey170 CG2162|FBan0002162|CT7070|
anon-EST:Posey173 CG9954|FBan0009954|CT28013|
anon-EST:Posey177 CG7221|FBan0007221|CT22265|
anon-EST:Posey179 Qm (CG17521|FBan0017521|CT38737|)
anon-EST:Posey18 CG12775|FBan0012775|CT36295|
anon-EST:Posey180 CG6617|FBan0006617|CT20578|
anon-EST:Posey185 CG8332|FBan0008332|CT24587| MERGE
anon-EST:Posey187 CG8395|FBan0008395|CT18601| MERGE
anon-EST:Posey188 CG7283|FBan0007283|CT22467|
anon-EST:Posey189 CG10186|FBan0010186|CT28647|
aligned AE003663 and AF171833; EST predicts
an additional exon at complement (<73055..73437)
anon-EST:Posey2 CG7701|FBan0007701|CT23463|
anon-EST:Posey20 CG16947|FBan0016947|CT37598|
(aligned AF171768 to AE003613, alignment extends
further than shown in our BLAST output)
anon-EST:Posey203 miple (CG1221|FBan0001221|CT2033|)
anon-EST:Posey205 CG9905|FBan0009905|CT27898|
anon-EST:Posey213 vimar (CG3572|FBan0003572|CT12008|)
anon-EST:Posey214 CG11752|FBan0011752|CT5038|
anon-EST:Posey219 CG7361|FBan0007361|CT22681|CT31879|
anon-EST:Posey224 CG1746|FBan0001746|CT5086|
anon-EST:Posey227 CG9394|FBan0009394|CT26667|
(extends CG at 3' end)
anon-EST:Posey228 CG7630|FBan0007630|CT23291| MERGE
anon-EST:Posey230 CG1552|FBan0001552|CT4006|
(check intron-exon boundaries of CG)
anon-EST:Posey231 CG17753|FBan0017753|CT11457|
(aligned AF083312 to AE003830; alignment extends
further than in our BLAST output)
anon-EST:Posey234 CG6783|FBan0006783|CT21061|
anon-EST:Posey235 BcDNA:GH07626 (CG3523|FBan0003523|CT11871|)
anon-EST:Posey237 CG17515|FBan0017515|CT33382|
(AF171847 aligned to AE003066, extends CG)
anon-EST:Posey240 smt3 (CG4494|FBan0004494|CT14617|)
anon-EST:Posey242 CG9282|FBan0009282|CT26439|
anon-EST:Posey244 CG12840|FBan0012840|CT31972|
anon-EST:Posey245 CG4169|FBan0004169|CT13760|
anon-EST:Posey250 CG7239|FBan0007239|CT22327|
anon-EST:Posey253 CG1837|FBan0001837|CT5608|
anon-EST:Posey256 CG1545|FBan0001545|CT4000|
anon-EST:Posey261 CG4561|FBan0004561|CT14730|
anon-EST:Posey265 Transferrin (CG6186|FBan0006186|CT19250|)
anon-EST:Posey266 CG3229|FBan0003229|CT10811|
(differs from CG at 3' end but sequence matches scaffold
look for alternate splice or correction of CG sequence)
anon-EST:Posey267 CG9240|FBan0009240|CT26394|
(extends CG at 3' end)
anon-EST:Posey272 CG17737|FBan0017737|CT2632|
anon-EST:Posey275 CG5537|FBan0005537|CT17516|
anon-EST:Posey276 CG3203|FBan0003203|CT10544|
anon-EST:Posey279 CG9473|FBan0009473|CT26832|
anon-EST:Posey281 CG11943|FBan0011943|CT35760|
anon-EST:Posey282 CG12014|FBan0012014|CT1651|
anon-EST:Posey284 CG15494|FBan0015494|CT35596|
anon-EST:Posey287 CG11388|FBan0011388|CT31798|
anon-EST:Posey29 CG6673|FBan0006673|CT20732|
anon-EST:Posey291 BM-40/SPARC (CG6378|FBan0006378|CT19876|)
anon-EST:Posey293 RecQ5 (CG4879|FBan0004879|CT15495|) AF171784 aligned to RecQ
anon-EST:Posey295 CG10423|FBan0010423|CT29278|
anon-EST:Posey3 CG9686|FBan0009686|CT6802|
(AF171762 aligned to AE003448)
anon-EST:Posey31 CG8398|FBan0008398|CT24665|
(AF171771 aligned to AE003562; extends last exon)
anon-EST:Posey36 EG:115C2.12 (CG18451|FBan0018451|CT32691|)
AF171773 aligned to AL031581
anon-EST:Posey39 CG2099|FBan0002099|CT6814|
anon-EST:Posey4 eIF-1A (CG8053|FBan0008053|CT24166|)
anon-EST:Posey40 CG4071|FBan0004071|CT13482| (EST extends CG4071)
anon-EST:Posey42 CG5687|FBan0005687|CT8701|
anon-EST:Posey43 BcDNA:GH07626 (CG3523|FBan0003523|CT11871|)
anon-EST:Posey45 CG4692|FBan0004692|CT15135|
anon-EST:Posey47 CG10320|FBan0010320|CT28984|
merge with anon-EST:Posey84
anon-EST:Posey49 CG5972|FBan0005972|CT18757|
anon-EST:Posey50 AP-50 (CG7057|FBan0007057|CT21823|)
anon-EST:Posey54 CG11376|FBan0011376|CT31756|
anon-EST:Posey62 CG3214|FBan0003214|CT10813|
anon-EST:Posey63 CG8415|FBan0008415|CT24703|
anon-EST:Posey66 CG5321|FBan0005321|CT16936|
anon-EST:Posey73 RpL29 (CG10071|FBan0010071|CT28349|) (aligned AF083519 with U40226)
anon-EST:Posey76 CG8309|FBan0008309|CT24557|
anon-EST:Posey8 CG3792|FBan0003792|CT12669|
anon-EST:Posey81 CG2176|FBan0002176|CT6332|
anon-EST:Posey84 CG10320|FBan0010320|CT28984| AF171790
merge with anon-EST:Posey47
anon-EST:Posey85 CG15067|FBan0015067|CT34938|
anon-EST:Posey87 CG5903|FBan0005903|CT18297|
anon-EST:Posey91 CG8844|FBan0008844|CT9259|
BEST:CK00325 Sur (CG5772|FBan0005772|CT18104|)
BEST:CK00230 KdelR (CG5183|FBan0005183|CT16555|)
BEST:CK00246 CG13920|FBan0013920|CT33459|
BEST:CK00459 CG8083|FBan0008083|CT8107|
BEST:CK00539 CG5912|FBan0005912|CT15575|
BEST:CK01110 CG16982|FBan0016982|CT32695|
BEST:CK01140 CG2165|FBan0002165|CT6738|
BEST:CK01209 CG9085|FBan0009085|CT26050|
BEST:CK01227 CG14709|FBan0014709|CT34500|
BEST:CK01296 CG5885|FBan0005885|CT18469|
BEST:CK01510 CG2768|FBan0002768|CT9403|
BEST:CK01577 CG12789|FBan0012789|CT37157|
BEST:CK02137 CG11163|FBan0011163|CT31188|
BEST:CK02213 CG3814|FBan0003814|CT12775|
BEST:CK02248 Tunen (CG8805|FBan0008805|CT3034|)
BEST:CK02288 CG2165|FBan0002165|CT6738|
BEST:CK02318 CG7144|FBan0007144|CT22073|
BEST:CK02467 CG11592|FBan0011592|CT33137|
BEST:LD04728 CG11546|FBan0011546|CT36453|
BEST:LD04967 l(2)k05815(CG2207|FBan0002207|CT7302|)
BEST:LD04971 CG11045|FBan0011045|CT28033|
BEST:LD06340 yoyo transposon
BEST:LD07107 AE003529.2:57569..58140
BEST:LD07122 CG9418|FBan0009418|CT26718|
BEST:LD08487 CG12253|FBan0012253|CT15065|
BEST:LD09360 nonA-l (CG10328|FBan0010328|CT28998|) (AA390491 aligned to nonA-l)
BEST:LD12308 The 5' and 3' ends of this EST AA438512 align with CG3171 Trehalose
BUT the middle has many mismatches. suspect.
BEST:LD12957 CG10528|FBan0010528|CT37301|
BEST:LD13681 CG16833|FBan0016833|CT15001|
BEST:LD14744 CG7832|FBan0007832|CT23772|
BEST:LD14959 CG8677|FBan0008677|CT5294|
BEST:LD23852 CG3558|FBan0003558|CT11970|
BEST:LD27171 BG:DS09218.3 (CG4455|FBan0004455|CT14482|)
BEST:LD29214 CG8290|FBan0008290|CT24533|
BEST:LD29743 CG4747|FBan0004747|CT15275| (mismatches in 5' 113 bp of EST, then OK)
BEST:LD29847 CG9539|FBan0009539|CT26986|
BEST:LD30049 CG5704|FBan0005704|CT2731|
BEST:LD32772 Hsc70Cb (CG6603|FBan0006603|CT39144|)
BEST:LD33989 CG5981|FBan0005981|CT18793|
(this EST listed as evidence)
Please add:
BEST:LD13441 (Genbank acc. AA439017) CG14478|FBgn0034222|CT34189|
___________________________________________________________________
nc6
abo CG6093|FBgn0032323|CT19161|
based on sequence sent by Dr. Pimpinelli (FBrf0129572).
anon-18DEa CG14224|FBan0014224|CT33839|
anon-18DEb CG14226|FBan0014226|CT33841|
anon-18DEd CG14233|FBan0014233|CT33849|
anon-18DEe CG14230|FBan0014230|CT33846|
anon-61C this is 'interband DNA', shouldn't be assigned to a CG gene
anon-85Da CG16750|FBan0016750|CT32111| (alignment extends CG at 5' end)
anon-85Db this is DNA AE003682:113634..114395, 102059.. 103900,103923..104221
1st segment flipped with respect to rest
anon-a 1-173 of 250 matches CG-less sequence on AE003483
no CT immunoglobin switch region-like.
anon-f CG1077|FBan0001077|CT1429|
anon-FF CG6156|FBan0006156|CT19304|CT19330
anon-ft1 region of chromosomal breakpoint, DO NOT assign CG's,
but can note that it aligns with the region containing
CG3086 and CG15770 (AE003435:135304..137515)
anon-Liu CG17270|FBan0017270|CT35903|
anon-OV1 phr (CG11205|FBan0011205|CT31302|)
(accession D26136 identical to accession S73530 listed under
phr)
anon-Pen16 clone may be chimeric
[CG12136|FBan0012136|CT7794|]
(1st 65 bp don't match CG12136,
1st 65 bp matches CG17251|FBan0017251|CT35403|)
BcDNA:LD22118 CG4411|FBan0004411|CT14362|
BcDNA:LP06355 Cyp304a1 (CG7241|FBan0007241|CT22337|)
chitin-synthase CG7464|FBan0007464|CT22967|
CycK CG15218|FBan0015218|CT35154
Dtf-1 TransFac entry only, not characterized molecularly
(binds Antp promoter)
EB1 CG3265|FBan0003265|CT10989|
Ec3 AE003809:237082..237118 matches 1-37
AE003799:38783..38907 matches 38-160
EG:BACR7A4.7 CG11639|FBan0011639|CT34386|
(following transcript and translation provided by Takis Benos,
not in EMBL/GB entry AL109630:>BACR7A4.7 drosophila melanogaster (fruit fly). transcription initiation factor iia gamma chain (tfiia p14 subunit) (tfiia-14) (dtfiia-s) (tfiia-gamma).
atgaactatcaacattacagggccacaacgctgggcagaacgctccagga
cactttggatgagatgatggagaggggcgatataaccaagaagattgcta
atttggttttactaagatatgacaagagcatttcaacagctctcaaggat
catggcacgagcaatatgtcctttacggccgaaagactggaaacctttag
atgctgcgacaatgtgtggactctgatcctaaaggacgcggagttccgcg
aggatcagcattccttgaaggtcgatgtggtcaaaattgtggcctgtctt
ggaactgacaatggaaatgaataa>BACR7A4.7 drosophila melanogaster (fruit fly). transcription initiation factor iia gamma chain (tfiia p14 subunit) (tfiia-14) (dtfiia-s) (tfiia-gamma).
MNYQHYRATTLGRTLQDTLDEMMERGDITKKIANLVLLRYDKSISTALKD
HGTSNMSFTAERLETFRCCDNVWTLILKDAEFREDQHSLKVDVVKIVACL
GTDNGNE*
Eip63F-2 matches CG-less sequence on AE003479
('Coding sequence unknown, according to accession U27300')
putative partial translation given in paper [FBrf0083007],
no match to it among predicted proteins.
fok - CG10746|FBan0010746|CT30111|
possibly untranslated
CT translation not available
Gebf-I TransFac entry only, not characterized molecularly
Hemagglutinin no matches in AE sequences, only other match is
nt 74-219 matches 1-146 of Influenza A virus
hrt P insertion site flank
matches CG-less sequence at AE003677:143024..143516
LB27 MERGE with yoyo; matches yoyo retrotransposon LTR
lectin-24Da CG-less (U. Theopold, personal comm. curated by Camb.)
lectin-24Fa CG-less (U. Theopold, personal comm. curated by Camb.)
lectin-24Fb CG-less (U. Theopold, personal comm. curated by Camb.)
MS:DS01001 this is a collection of many accessions characterizing
repeat regions
Myc does not align with any other Drosophila DNA in GenBank,
BLAST with nr (non-redundant) and dbEST databases.
some alignment with unfiltered BLAST: possible repeat
element?
Pglym87 [CG17645|FBan0017645|CT28399]
possible PSEUDOGENE as per FB gene report
(Currie and Sullivan, 1994).
Pk17E CG7001|FBan0007001|CT21577|
Pk36A grp (CG17161|FBan0017161|CT14720|)
Pk53C Cdk4/6 (CG5072|FBan0005072|CT15896|)
Pk91C CG7719|FBan0007719|CT23435|
RpL12 >CG3195|FBgn0034968|
(PROBLEM: RpL12 has been mapped to 62E, CG3195 to 60B2-3)
CG3195 and CG10485 are transcribed off opposite strands,
RpL12 doesn't have a CDS annotated, check with other organisms:>CG3195|FBgn0034968
MPPKFDPTEVKLVYLRCVGGEVGATSSLAPKIGPLGLSPKKIGDDIAKAT
SDWKGLKITVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKQKNIKH
SGNIGFEDILAIARVMRPRSMARELKGTCKEVLGTAQSVGCTVDGKHPHD
VIDELNEGSIEVPAE
>CG10485|FBgn0034969
MDLGLITRAMARMSSKPMFPLCLTSRIAGQYSLFFCFLRSRGGSFRALMI
SEAAEGTTEMAACRFWMVRQTVIFRPFQSEVALAMSSPIFLGDYRETLLL
ARIAQVNKPICMLTRPRGPIFGAREDVAPTSPPTQRRYTVIWVQKFVIED
NPLL
Mouse RpL12:>gi|398048|gb|AAA40066.1| ribosomal protein L12
MPPKFDPNEVKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKAT
GDWKGLRITVKLTIQNRQAQIEVVPSASGLIIKALKEPPRDRKKQKNIKH
SGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHPHD
IIDDINSGAVECPAS
RpL31 CG1821|FBan0001821|CT5526|
sw59 lola (CG12052|FBan0012052|)
ted only accession listed is a short putatively intronic fragment
of 70 bp (aligns to AE003672:152669..152738)
_____________________________________________________________________
The correspondence of the following Ugt genes to CG genes were
verified by Dr. Uli Theopold:
Ugt58Fg CG4414
Ugt36Ba CG13270
Ugt36Bb CG13271
Ugt36Bc CG17932
Ugt37b1 CG9481
Ugt86Da CG18578
Ugt86Db CG6649 (probably a polymorphic variant of Ugt35b, see FBrf0110927)
Ugt86Dc CG4739
Ugt86Dd CG6633
Ugt86De CG6653
Ugt86Df CG6644 (probably a polymorphic variant of Ugt35a, see FBrf0110927)
Ugt86Dg CG17200
Ugt86Dh CG4772
Ugt86Di CG6658
Ugt86Dj CG15902
_____________________________________________________________________
Vha100-1 BcDNA:LD21248 (CG1709)
Vha100-2 BcDNA:LD21735 (CG18617)
Vha100-3 author queried Aug.25 (whole contig accession is given
in paper; coordinates unknown)
Vha16-2 author queried Aug.25 ''
Vha16-3 author queried Aug.25 ''
Vha16-4 author queried Aug.25 ''
VhaAC39 CG2934|FBan0002934|CT9953|
VhaM9.7-1 CG11589|FBan0011589|CT36548
VhaM9.7-2 CG7625|FBan0007625|CT23265
VhaPPA1-1 CG7007|FBan0007007|CT21672
VhaPPA1-2 author queried Aug.25
yip1 CG18497|FBan0018497|CT42170|
yip4 matches CGless sequence on AE003519:250616..251056
Addenda to nc6 list>From FBrf0108062
gene accession Celera gene
BEST:LD25345 AA941286 CG17322
BEST:GH06505 AI107184 CG17324
BEST:GH09393 AI109977 CG4302
BEST:GM04645 AA695862 CG18578 (matches Ugt86Da)
AntP450 = Cyp6w1 (CG8345)
AntP450 dentified with: GH06928 accession AI113367
which aligns perfectly with CG8345 corresponding to Cyp6w1
(AI113367 is listed among the evidence for Cyp6w1)
Ugt37a1 CG11012
(DS51087 complement 6570..68193)
EfSec CG9841
(Tujebajeva et al 2000 EMBO reports 1(2)158-163)
robl22E CG10838|FBan0010838|CT30347|
robl37BC CG15171|FBan0015171|CT35080|
robl62A CG1014|FBgn0035222|CT1028|
BEST:CK02567 CG5661|FBan0005661|CT17880|
BEST:CK02623 CG15438|FBan0015438|CT35502|
BEST:CK02656 CG3164|FBan0003164|CT10462|
BEST:GM02209 CG3696|FBan0003696|CT12335|
BEST:GM02553 CG6530|FBgn0034220|CT20339| accession AA695295
BEST:GM10514 CG10161|FBan0010161|CT28571|
BEST:HL03644 CG5707|FBan0005707|CT2751|
BEST:HL04053 CG1079|FBan0001079|CT1463| (extends CG at 5' end)
BEST:LD02456 matches CG-less at AE003761:145689..145157
BEST:LD03274 lola (CG12052|FBan0012052|CT40980|)
BEST:LD03829 homer (CG11324|FBan0011324|CT31607|)
BEST:LD04728 CG11546|FBan0011546|CT36453|
BEST:LD21971 CG11518 (please add accession AA817007)
CaBP1 BG:DS09218.4 (CG5809|FBan0005809|CT18216|)
(aa seq from FBrf0104763, matched by BLASTP)
Las CG5231
by BLASTN alignment with AA820940 and AA201873 [FBrf0111379]
RpL37a CG5827
sequence in [FBrf0111872], not submitted to GB, adjacent to qtc
att CG4241|FBan0004241|CT13930|
sequence in [FBrf0089733] but not in GenBank
Celera translation is further 5' than the one in [FBrf0089733]
primo-1 and primo-2 correspond to CG9599 (based on predicted peptide
in FBrf0125124).CG9599 has to be split and intron-exon structure corrected.
qtc CG14039|FBan0014039|CT33598|
sequence in FBrf0127087 but not in GenBank
Gyk CG18374 (curator inference)
According to FBrf0103348 figure 3 NitFhit is in the
intron of Gyk (opp.strand). BLASTP of predicted translation
of CG18374 gives many hits to glycerol kinases (top 5 below)
gb|AAF47346.1| (AE003467) CG18374 gene product [Drosophila ... 1038 0.0
ref|NP_034424.1| glucokinase activity, related sequence 2 >... 549 e-155
ref|NP_032220.1| glycerol kinase >gi|2493484|sp|Q64516|GLPK... 543 e-153
emb|CAB54858.1| (AJ252550) glycerol kinase [Homo sapiens] 542 e-153
sp|Q63060|GLPK_RAT GLYCEROL KINASE (ATP:GLYCEROL 3-PHOSPHOT... 542 e-153
Lip2 CG17116 (curator inference)
[FBrf0102171] states Lip2 is about 1 kb away from Lip1
Lip2+ anon-32Aa- Lip2+ Lip1+
[FBrf0102171] states that Lip2 may be nonfunctional
GHSQV is GHSQA in Celera sequence
anon-32Aa CG6415 (curator inference)
[FBrf0102171] states that there is an aminomethyltransferase
subunit in the putative 3rd intron of Lip2 (FB symbol anon-32Aa).
ND23 CG3944 (curator inference)
(ND23 is a NADH dehydrogenase adjacent to spn-E
order ND23- spn-E+)
Sti1 Hop (CG2720) curator inference
Hop is listed in the accession AF056198
as being a 'yeast Sti1p homolog'
Detailed molecular map given in Current Biol 9:1019 [FBrf0111517]
smo+ U2af38- Sti1+ Pi3K21B+ Plc21C+
CG2720 is between U2af38 and Pi3K21B.
pkaap BG:DS02740.4 (CG4132) curator inference
CG4132 has homology to protein kinase A anchoring proteins
adjacent to crp and on opposite strand
[FBrf0110073] order twe- crp- pkaap+ (additional gene predicted betw.
twe and crp in Celera and BDGP sequences)
snRNP69D CG10753 curator inference
gene order from [FBrf0086377] snRNP69D- Ptp69D+ Klc-
stated to be 1 kb upstream from and transcribed in opposite direction
from Ptp69D. CG10753 shows homology to small nuclear ribonucleoproteins