RetrogeneDB ID:

retro_tbel_1419

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:GeneScaffold_4651:248787..250538(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:U2SURP
Ensembl ID:ENSTBEG00000016313
Aliases:None
Description:U2 snRNP-associated SURP domain containing [Source:HGNC Symbol;Acc:30855]


Retrocopy-Parental alignment summary:






>retro_tbel_1419
ATGGCGGACAAACGCCAGGCGGCTCTCAGAGGCCAGTTCAAGACCAGATCATCAGATGTCATCATCTGGATCTCAGATGC
GCATATGGACGCATCTGACCTCGATAGATGTGGGTCGAGTTCGACACGACCTAAGAGCCCAAGGAAACATAATTACAGGA
GTGAAATGTGCCCGTGAGAGCCTTTATGATTCTCCTCATCAGAATCTCTCAAAACCTCTCTTAGAAAACAAACTTAATGC
ATTCAGTATTGGAAAAATGAGTACAGCTAAGTGAACTTTAAGCAAGAAGGAACAAGAAGAATTAAAGAAAAAGGAGGATG
AAAAGGCAGCTGCTGAGATTTATGAGGAATTTCTTGCTGCTTTTGAAGGAAGTGATGGTAATAAAGTGAAAACATTTGTA
CGAGGAGGTGTCGTTAATGCAGCTAAAGAAGAACATGAAACAGATGAAAAAAGAGGTAAAATCTATAAGCCATCTTCAAG
ATTTGCAGATCAAAAGAACCCTCCAAATCAGTCATCCAATGAAAGACCACCATCTCTTCTTGTGATAGAAACCAAAAAGC
CTCCACTGAAGAAAGGGGGGAAAGAAAAGAAAAAAAGCAATTTGGAACTCTTCAAAGAAGAATTAAAACAAATTCAAGAA
GAGCGTGATGAGAGACATACAACTAAAGGCAGGTTAAGTCGATTCGAGCCTCCTCAGTCAGATTCTGACGGTCAGTGCCG
TAATATGGATGCGCCTTCAAGAAGAAATAGATCATCTGTTCTTGATGATTATGTCCCTGGCTCACACGATGTAGGAGATC
CAAGCACCACTAATTTATATCCGGGAAACATTAATCCACAGATGAATGAAGAAATGCTGTGCCAAGAATTTGGGAGATTT
GGACCAATAGCCAGTGTGAAAATTATGTGGCCTAGAACTGATGAAGAAAGAGCAAGAGAGTGAAACTGTGGCTTTGTGGC
TTTTATGAATAGAAGAGATGCTGAAAGGGCTTGGAAAAATTTAAATGGAAAAATGATAATGTCATTTGAAATGAAGTCAG
GTTGGGGTAAAGCTGTACCTATTCCTCCACACCCAATATACATTCCGCCTTCTATGATGGAACATACGCTTCCCCCACCT
CCATCTGGACTGCCATTTATCGCACAGCCTAGAGAACGGTTGAAAAACCCCAATGCTCCCATGTTACCGCCACCTAAAAA
CAAGGAGGATTTCGAGAAGACTCTGTCGCAAGCCATAGTCAAAGCGGTTATCCCAACAGAAAGGAATTTGCTCGCCCTGA
TACATCGAATGATAGAGTTTGTTGTACGTGAAGGGCCAATGTTTGAAGCTATGATTATGAACAGAGAAATCAACAATCCT
ATGCTCAGGTTCTTATTTGAAAATCAGACACCAGCCCACGTTTACTATAGGTGGAAGCTTTATTCTATTCTTCAGGGAGA
TTCTCCAACGAAGTGGCGGATGGAAGATTTTCATATGTTCAAAAATGGATCTTTTTGGAGGCCACCACCATTAAATCCAT
ACCTGCATGGGATGTCAGAAGAGCAGGAAACAGAAGCTTTTGTAGAAGAGCCTAGTAAAAAGGGAGCACTTAAGGAAGAA
CAGAGGGACAAATTAGAAGAAATCCTGCGGGGATTAACTCCAAGAAAAAAATGACATTGGAGATGCAATGGTTTTCTGTC
TCAATAATGCTGAAGCTGCTGAAGAAATAGTGGATTGCATTACTGAGTCGTTGTCCATCTTAAAGACCCCT

ORF - retro_tbel_1419 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.14 %
Parental protein coverage: 56.9 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMADK-TPGGSQK-ASSKTRSSDVHSSGS-SDAHMDASGPSDSDMPSRTRPKSPRKHNYRNES-ARESLCD
MADK.TPGGSQ..ASS........SSGS.SDAHMDAS...D....S.TRPKSPRKHNYR.E..ARESL.D
RetrocopyMADK<TPGGSQR<ASSRP-DHQMSSSGS<SDAHMDASD-LDRCGSSSTRPKSPRKHNYRSEM>ARESLYD
ParentalSPHQNLSKPLLENKLKAFSIGKMSTAKRTLSKKEQEELKKK-DGKAAAEIYEQLLAAFE-SDGNKVKTFV
SPHQNLSKPLLENKL.AFSIGKMSTAK.TLSKKEQEELKKK.D.KAAAEIYE..LAAFE.SDGNKVKTFV
RetrocopySPHQNLSKPLLENKLNAFSIGKMSTAK*TLSKKEQEELKKKEDEKAAAEIYEEFLAAFEGSDGNKVKTFV
ParentalRGCVVNAAKEEHETDEKRGKIYKPSSRFADQKNPPNQSSNERPPSLLVIETKKPPLKKGEKEKKKSNLEL
RG.VVNAAKEEHETDEKRGKIYKPSSRFADQKNPPNQSSNERPPSLLVI.................NLEL
RetrocopyRGGVVNAAKEEHETDEKRGKIYKPSSRFADQKNPPNQSSNERPPSLLVIXXXXXXXXXXXXXXXXXNLEL
ParentalFKEELKQIQEERDERHKTKGRLSRFEPPQSDSDGQRRNMDAPSRRNRSSGVLDDYAPGSHDVGDPSTTNL
FKEELKQIQEERDERH.TKGRLSRFEPPQSDSDGQ.RNMDAPSRRNRSS.VLDDY.PGSHDVGDPSTTNL
RetrocopyFKEELKQIQEERDERHTTKGRLSRFEPPQSDSDGQCRNMDAPSRRNRSS-VLDDYVPGSHDVGDPSTTNL
ParentalYLGNINPQMNEEMLCQEFGRFGPLASVKIMWPRTDEERARERNCGFVAFMNRRDAERALKNLNGKMIMSF
Y.GNINPQMNEEMLCQEFGRFGP.ASVKIMWPRTDEERARE.NCGFVAFMNRRDAERA.KNLNGKMIMSF
RetrocopyYPGNINPQMNEEMLCQEFGRFGPIASVKIMWPRTDEERARE*NCGFVAFMNRRDAERAWKNLNGKMIMSF
ParentalEMKLGWGKAVPIPPHPIYIPPSMMEHTLP--PSSLH--AQPRERLKNPXXXXXXXXXXXXXXXXTLSQAI
EMK.GWGKAVPIPPHPIYIPPSMMEHTLP..PS.L...AQPRERLKNP................TLSQAI
RetrocopyEMKSGWGKAVPIPPHPIYIPPSMMEHTLPPPPSGLPFIAQPRERLKNPNAPMLPPPKNKEDFEKTLSQAI
ParentalVKVVIPTERNLLALIHRMIEFVVREGPMFEAMIMNREINNPMFRFLFENQTPAHVYYRWKLYSILQANSP
VK.VIPTERNLLALIHRMIEFVVREGPMFEAMIMNREINNPM.RFLFENQTPAHVYYRWKLYSILQ..SP
RetrocopyVKAVIPTERNLLALIHRMIEFVVREGPMFEAMIMNREINNPMLRFLFENQTPAHVYYRWKLYSILQGDSP
ParentalTKWRTEDFRMFKNGSFWRPPPLNPYLHGMSEEQETEAFVEEPSKKGALKEEQRDKLEEILRGLTPRK-ND
TKWR.EDF.MFKNGSFWRPPPLNPYLHGMSEEQETEAFVEEPSKKGALKEEQRDKLEEILRGLTPRK.ND
RetrocopyTKWRMEDFHMFKNGSFWRPPPLNPYLHGMSEEQETEAFVEEPSKKGALKEEQRDKLEEILRGLTPRK>ND
ParentalIGDAMVFCLNNAEAAEEIVDCITETLSILKTP
IGDAMVFCLNNAEAAEEIVDCITE.LSILKTP
RetrocopyIGDAMVFCLNNAEAAEEIVDCITESLSILKTP

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tupaia belangeri was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tbel_1419 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_1419 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Myotis lucifugus ENSMLUG000000029201 retrocopy
retro_mluc_276,
Tupaia belangeri ENSTBEG00000016313 1 retrocopy
retro_tbel_1419 ,




Copyright © RetrogeneDB 2014-2017