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Bayraktaroglu, L. (2000.11.2). Current list of possibly CG-able known genes. 
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FBrf0131225
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Personal communication to FlyBase
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Text of Personal Communication
From leyla@XXXX Thu Nov 02  01:19:12  2000
Envelope-to: ag24@XXXX
Delivery-date: Thu, 2 Nov 2000  01:19:12  +0000
Date: Wed, 1 Nov 2000  20:18:24  -0500 (EST)
From: Leyla Bayraktaroglu <leyla@XXXX>
Reply-To: Leyla Bayraktaroglu <leyla@XXXX>
Subject: Current list of possibly CG-able known genes
To: ag24@XXXX
Cc: curatorsXXXX, joelXXXX
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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
DOI
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