RetrogeneDB ID:

retro_ttru_1309

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_110149:226559..228046(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CDC20
Ensembl ID:ENSTTRG00000010813
Aliases:None
Description:cell division cycle 20 [Source:HGNC Symbol;Acc:1723]


Retrocopy-Parental alignment summary:






>retro_ttru_1309
ATGGCCCAGTTCGTGTTCGAGGGTGACCTGCACTTGCTGCTGCAGCCGGCTACACCCATGCCCAGCGCAGCCCCTGCGTG
CTGGCAGCGCAAAGCGAAGGAAGCTTCGGGCCGGGCCCCTCGCCTATGTGGGCAGCCAACCGATCCCACAGCGCCGGGAG
GACCCCGGGGCCGAACTCCCGGCAAATCCAGCTCCAAGATTCAGACCACTCCCGGCAAACCTGGCGGCAATCGCTCTATC
CCCCGTCGCAGTGCTTCCCAGATGGAGGTCGCTAGTATTCTCCCGAGCAAGGAGAAGCAGCCCGAAGACAGTCAGACACC
CACCAAGAAGGAACATCAGAAAGCATGGGCTTTGAACCTGAACGGTTTTCATATGGAGGAAGCCAAGATGCTTCGGCTCA
GTGGAAAACCACAAAATGCCCCAGAAGGTTACCAGAACAGACTGAAAGTACTCTGTAGCCAGAAGGCCACGCCCAGCTCC
AGCAGGAAGACCAGCAGTTACATTCCTTCGCGGCCAGACAGGATCCTGGACGCCCCTGAAATCCGGAATGACTAGTACCT
GAACCGTGTAGATTGGAGCTCTGGGAATATACTGGCTGTGGCTTTGGACAACAGTGTGTACTTGTGGAGTGCTAGCTCTG
GTGACACCCTGCAGCTGCTGCAACTGGAGCAGCCTGGGGACTATACATCTTCTGTGGCCTCGATCAAGGAGGGAAACTAC
CTGGCTGTGGGTACCAGCAGTGCTGAGGTGCAGCTGCGGGATGTACAACAGCAGAAACGGCTTCGAAACATGACCATTCT
GCCCGAGTGGGCTCCCTCGGTTGGAATAGCTATATCCTGTGTAGTGGCTCACTCTCTGGCCACATCCCACACCATGATGT
TCGGGTAGCAGAACACCATGTGGCCACACCGAGTGGCCACAGCCAGGAAGTGTGTGGTCTGCGCTGGGCCCCAGATGGAC
GACATTTAGCCAGTGGCGGCAACGATAACTTGGTCGACGTGTGGCCCAGTGCTCCTGGAGAGGGTGGCTGGGTTCCTCTG
CAGACATTCACCCAGCATCAAGAGGCTATCAAGGCTGTGGCTTGGTGTCCCTGGCAACCCAATGTCCTGGCAACTGGAGG
GGGCACAAGTGATCGACACATTCGTGTCTGGAACGTCTGCTCTGGGGCCTGTCTGAGTGCTGTGGATGCCCATTCCCAGG
TGTGCTCCATCCTCTGTTCTCCCCACTAGAAGGAGCTCATCTCAGGCCATGGCTTTGCCCAGAAACAGCTGGTGATTTGG
AACCCAACCATGGCCAAGGTGGCTGAGCTGAAAGGTCACACAGCCCAGGTCCTTAGCCTGACCATGAGCCCAGATGGGGC
TACAGTGGCATCAGCAGCAGCAGATGACACCCTGTGGCTGTGGTGCTGCTTTGAGTTGGACCCTGCCCGGCGGCGGGAGC
GGGAGAAGGCCAGCACAGCACAAAGCAGCCTCACCCACCAGGGCATC

ORF - retro_ttru_1309 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.63 %
Parental protein coverage: 99.8 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAQFVFESDLHSLLQLDTPIPNAPPARWQRKAKEAAG-PAPSPMRAANRSHSAGRTPG-RTPGKSSSKNQ
MAQFVFE.DLH.LLQ..TP.P.A.PA.WQRKAKEA.G.P.PSPM.AANRSHSAGRTPG.RTPGKSSSK.Q
RetrocopyMAQFVFEGDLHLLLQPATPMPSAAPACWQRKAKEASG<PGPSPMWAANRSHSAGRTPG>RTPGKSSSKIQ
ParentalTTPSKPGGDRYIPHRSASQMEVASFLLSKENQPEDSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQ
TTP.KPGG.R.IP.RSASQMEVAS.L.SKE.QPEDSQTPTKKEHQKAWALNLNGF..EEAK.LRLSGKPQ
RetrocopyTTPGKPGGNRSIPRRSASQMEVASILPSKEKQPEDSQTPTKKEHQKAWALNLNGFHMEEAKMLRLSGKPQ
ParentalNAPEGYQNRLKVLYSQKATPSSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYL
NAPEGYQNRLKVL.SQKATPSSSRKT..YIPS.PDRILDAPEIRND.YLN.VDWSSGN.LAVALDNSVYL
RetrocopyNAPEGYQNRLKVLCSQKATPSSSRKTSSYIPSRPDRILDAPEIRND*YLNRVDWSSGNILAVALDNSVYL
ParentalWSASSGDILQLLQLEQPGDYISSVAWIKEGNYLAVGTSSAEVQLWDVQQQKR-LRNMTSHSARVGSLCWN
WSASSGD.LQLLQLEQPGDY.SSVA.IKEGNYLAVGTSSAEVQL.DV.QQ.........HSARVGSL.WN
RetrocopyWSASSGDTLQLLQLEQPGDYTSSVASIKEGNYLAVGTSSAEVQLRDV-QQQK<TASKHDHSARVGSLGWN
ParentalSYILSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVP
SYIL.SGS.SGHI.HHDVRVAEHHVAT.SGHSQEVCGLRWAPDGRHLASGGNDNLV.VWPSAPGEGGWVP
RetrocopySYILCSGSLSGHIPHHDVRVAEHHVATPSGHSQEVCGLRWAPDGRHLASGGNDNLVDVWPSAPGEGGWVP
ParentalLQTFTQHQGAVKAVAWCPWQPNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISG
LQTFTQHQ.A.KAVAWCPWQPNVLATGGGTSDRHIR.WNVCSGACLSAVDAHSQVCSIL.SPH.KELISG
RetrocopyLQTFTQHQEAIKAVAWCPWQPNVLATGGGTSDRHIRVWNVCSGACLSAVDAHSQVCSILCSPH*KELISG
ParentalHGFAQNQLVIWKYPTMAKVAELKGHTARVLSLTMSPDGATVASAAADETLRLWRCFELDAARRREREKAS
HGFAQ.QLVIW..PTMAKVAELKGHTA.VLSLTMSPDGATVASAAAD.TL.LW.CFELD.ARRREREKAS
RetrocopyHGFAQKQLVIWN-PTMAKVAELKGHTAQVLSLTMSPDGATVASAAADDTLWLWCCFELDPARRREREKAS
ParentalAAKSSLIHQGI
.A.SSL.HQGI
RetrocopyTAQSSLTHQGI

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






RNA-Seq - click to see more details

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_1309 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1309 was not experimentally validated.

Retrocopy orthology:
Tursiops truncatus 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 10 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000066802 retrocopies
retro_chof_2172, retro_chof_2286,
Callithrix jacchus ENSCJAG000000034141 retrocopy
retro_cjac_1608,
Homo sapiens ENSG000001173991 retrocopy
retro_hsap_4187,
Gorilla gorilla ENSGGOG000000104191 retrocopy
retro_ggor_96,
Mus musculus ENSMUSG000000063981 retrocopy
retro_mmus_1536,
Nomascus leucogenys ENSNLEG000000134191 retrocopy
retro_nleu_2847,
Pongo abelii ENSPPYG000000014481 retrocopy
retro_pabe_3428,
Pan troglodytes ENSPTRG000000006341 retrocopy
retro_ptro_2843,
Tarsius syrichta ENSTSYG000000127033 retrocopies
retro_tsyr_1560, retro_tsyr_442, retro_tsyr_938,
Tursiops truncatus ENSTTRG00000010813 1 retrocopy
retro_ttru_1309 ,


Copyright © RetrogeneDB 2014-2017