Hello Jim, The track "EST" is sourced from NCBI - which we then align with BLAT. The sequences that you list appear to have not passed our alignment criteria so are not present in the UCSC Browser's May 2006 chicken (/Gallus gallus/) v2.1 draft assembly (galGal3). http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken&db=galGal3
The best way to have this data renamed/removed is to contact the original data submission scientist/group and have them submit a correction. It will then flow downstream to us and other users of Genbank sequence at a subsequent release. Your case will probably be relatively easy to make based on the data you have collected. Most of these have been released recently and older data is in general more difficult to track down & change. Jennifer Jackson UCSC Genome Bioinformatics Group Jim Johnson wrote: > Greetings - > > Note on probably genome mis-identification of CYP450 in Gallus gallus. It > appears a noted CYP4F that occurs within the EST database is more likely a > member of the CYP2E2 family. > > Name of assemblies (EST Blast): > > gb|CD735260.1| 4015378 1GAL - Chicken Intestinal Lymphocyte.. > gb|BG713654.1| pgl1n.pk010.m8 Normalized Liver Library Gallus.. > gb|BU124422.1| 603148196F1 CSEQCHL18 Gallus gallus cDNA clone.. > gb|CD763835.1| GGEZLB1006D03.g Limb Bud - LB1 Gallus gallus.. > gb|CD764153.1| GGEZLB1010D02.g Limb Bud - LB1 Gallus gallus.. > gb|CD731342.1| 4041128 1GAL - Chicken Intestinal Lymphocyte.. > > And from the following reference: > > http://drnelson.utmem.edu/chicken.FASTA.htm > > >> New CYP4F family member 63% to 4F22 CD735260 BU124422 CD731342 CD737432found >> by Jie Shen, Lei >> YangMVLSWLLVALLVALLVAWLRDAVVTVTRFRATCQQLRHFPLPPWRNWLLGHTGMARNTEEGLQDVDKVVAQYRHGCLWWLSPWLPILRLFHPDTLRPVLMASAFTAPKDKLFYGFLKPWLGDGLLLSRGDKWARHRRLLTPAFHFDILKSYVSIFNSSTHIMHTKWRAAAKAVGGPVGRNMMEDLSLLTLDTLQKCIFSHDSHCQEQRSEYIEAILELSTLVVRRQQRLLHHTSWLYRLSADGRRFARACATVHSFTANVVQRRRQELNHLGHQAWLKGRQGRSTDFIDLLLLTKDEDGNTLSDEDISAEADTFMFEGHDTTASGLAWLLYNLAHHPHYQEQCRQEVRELLKGRNVEEIEWEDLSLLPFTTMCIKESLRLHPPVTAVSRRCTEDIAMRDGRVIPKEVICLMSIYGTHHNPDIWPEPQVYDPLRFSPENSQGRSPLAFIPFSAGPRNCIGQSFAMAEMKVVAALTLARFAVRPDPARPVRRKSELILRAEDGLWLQLEPLSAMP* >> > > ------------------------------------------------------------ > Chromosome position unknown. This CYP450 has probably been misidentified in > Gallus gallus since it is most likely it is CYP2E2 and not a 4F family member. > > I am attaching a dendogram along with this email so you can see that the > position the Gallus gallus CYP2E2 appears correct. Protein sequences are > provided below for doing a sequence comparison. > > Thanks, hope this helps, > > Jim Johnson > Prattville, AL > > The protein sequences below can be used to run a clustal (note that a > corrupted polyA insert has been removed from T. guttata). > > >> gi|224154700|ref|XP_002198488.1| >> > PREDICTED: similar to cytochrome P450, family 2, subfamily E, polypeptide 2 > homolog [Taeniopygia guttata] > > MAVATALGSLGAVALGTFAVALLLQWLWNALLAVTRFRATCRQLNKFPIPPWRSWVLGHTGMVRSTEEGL > QQVDSLVARYRHGCLWWGLPWLPVLRLFHPSTLRPLLSASAFVAPKDKIFYGFLKPWLGEGLLLSGGERW > AQHRRLLTPAFHGDVLRNYLGIFNQSTRVLLAKWGRLAGGGPVELEVLQPLSLLTLDTLQKCIFSHESHC > QERPSEYIQAILELSSLVVRRQFRPLLHPWWLYRLSSDGRRFARACATVHNFTADVVQRRRRALTCLGHQ > ARLDGHQGHRMDFIDLLLLSKDENGHTLSDEDIAAEAETFMFEGHDTTASGLAWLFYNLAGHPEHQERCR > QEVQELLAGRDTADIEWEDLSQLPFTTMCIKESLRLHPPVTAVSRRCTEDIPLRDGRVIPKGVICLMSIY > GTHHNPDLWPEPEVFNPLRFSPENSKGRSPSSFIPFSAGPRNCIGQSFAMAEMKVVVALTLSRFVLRRDT > ARPPPRRKPELILRAEDGLWLLLEPLLAVP > > >> Proposed CYP4F family member 63% to 4F22 CD735260 BU124422 CD731342 CD737432 >> > > found by Jie Shen, Lei Yang > > [Predicted: Gallus gallus CYP2E2]: > > MVLSWLLVALLVALLVAWLRDAVVTVTRFRATCQQLRHFPLPPWRNWLLGHTGMARNTEEGLQDVDKVVA > QYRHGCLWWLSPWLPILRLFHPDTLRPVLMASAFTAPKDKLFYGFLKPWLGDGLLLSRGDKWARHRRLLT > PAFHFDILKSYVSIFNSSTHIMHTKWRAAAKAVGGPVGRNMMEDLSLLTLDTLQKCIFSHDSHCQEQRSE > YIEAILELSTLVVRRQQRLLHHTSWLYRLSADGRRFARACATVHSFTANVVQRRRQELNHLGHQAWLKGR > QGRSTDFIDLLLLTKDEDGNTLSDEDISAEADTFMFEGHDTTASGLAWLLYNLAHHPHYQEQCRQEVREL > LKGRNVEEIEWEDLSLLPFTTMCIKESLRLHPPVTAVSRRCTEDIAMRDGRVIPKEVICLMSIYGTHHNP > DIWPEPQVYDPLRFSPENSQGRSPLAFIPFSAGPRNCIGQSFAMAEMKVVAALTLARFAVRPDPARPVRR > KSELILRAEDGLWLQLEPLSAMP > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
