RetrogeneDB ID:

retro_ttru_1475

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_114210:90068..91495(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSTTRG00000004863
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBQLN1
Ensembl ID:ENSTTRG00000004696
Aliases:None
Description:ubiquilin 1 [Source:HGNC Symbol;Acc:12508]


Retrocopy-Parental alignment summary:






>retro_ttru_1475
GCTGCGGCCCAAAGCCCTGCCTCTGCCCCGGCGGAGCCCAAAATTATCAAAGTCACTGTGAAGACCCCCAAAGAGAAAGA
GGAGTTCGCAGTGCCCGAGAACAGCTCAGTCCAGCAGTTTAAGGAAGCGATTTCGAAACGCTTCAAATCCCAAACGGATC
AGCTAGTGCTGATTTTTGCCGGAAAAATCTTAAAAGATCAAGATACCTTGATTCAGCATGGCATCCATGATGGACTGACT
GTTCATCTTGTCATCAAAAGCCAGAACCGACCTCAGGGCCAGTCCACCCAGCCTAGTAATGCCGCGGGAACTAATACTAC
CACCGCGTCGACTCCCAGGAGTAACTCCACACCTATTTCCACAAATAGCAACCCGTTTGGGTTGGGGAGCCTGGGAGGAC
TTGCAGGCCTTAGCAGCCTGGGCTTGAGCTCGACCAACTTCTCTGAGCTCCAGAACCAGATGCAGCAGCAGCTCCTGTCC
AGCCCTGAGATGATGATCCAAATCATGGAAAATCCCTTTGTTCAGAGCATGCTTTCGAATCCTGATCTGATGAGGCAGCT
CATTATGGCCAATCCACAGATGCAACAATTGATTCAGAGAAACCCAGAAATTAGTCACCTGCTCAACAACCCAGATATAA
TGAGGCAGACCCTCGAAATCGCCAGGAATCCAGCTATGATGCAAGAAATGATGAGAAATCAAGACCTGGCTCTCAGCAAT
CTTGAAAGCATCCCAGGTGGCTACAATGCTTTACGGCGCATGTACACTGACATTCAAGAACCCATGCTAAATGCCGCACA
AGAGCAGTTTGGGGGTAATCCGTTTGCCTCGGTGGGGAGCAGTTCCTCCTCTGGGGAAGGTACGCAGCCTTCCCGCACAG
AAAATCGCGATCCACTACCCAATCCGTGGGCGCCACCACCGGCTACCCAGAGTTCTGCGACCACCAGCACAACAACGAGC
AGTGGCAGTGGATCTGGCACTAGCTCTAGCAGTGCTACGGGGAACACAGTGGCTGCAGCTAATTATGTTGCCAGCATCTT
CAGCACCCCAGGAATGCAGAGCTTGCTGCAACAGATAACTGAAAACCCCCAGCTGATCCAGAATATGCTGTCTGCACCCT
ATATGAGAAGCATGATGCAGTCGCTGACCCAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCTGTGTTTACT
GCAAATCTCAGCTGCAGGAGCAGATGCGTCCACAGCTCCCTGCTTTCCTGCAGCAGATGCAGAATCCAGACACACTCTCA
TCCATGTCAAACCCAAGAGCAATGCAGGCTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGG
CCTCATTCCAAGCTTCACTCCAGGTGTGGGGGTGGGGGTGCTGGGAACAGCTATAGGCCCTGTAGGC

ORF - retro_ttru_1475 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.42 %
Parental protein coverage: 81.25 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAPAAAAAAASTEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTL
A.A...A.A..EPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFKS.TDQLVLIFAGKILKDQDTL
RetrocopyAAAQSPASAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTL
ParentalSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTSGSNATASSAPNSNSTSGSATSNPFGLGGLGGLAGLSSL
.QHGIHDGLTVHLVIK.QNRPQ..S.Q..N..G.N.T..S.P.SNST..S..SNPFGLG.LGGLAGLSSL
RetrocopyIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTTASTPRSNSTPISTNSNPFGLGSLGGLAGLSSL
ParentalGLNTTNFSELQSQMQRQLMSNPEMMVQIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHMLNN
GL..TNFSELQ.QMQ.QL.S.PEMM.QIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISH.LNN
RetrocopyGLSSTNFSELQNQMQQQLLSSPEMMIQIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHLLNN
ParentalPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQEPMLSAAQEQFGGNPFASLVS
PDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQEPML.AAQEQFGGNPFAS..S
RetrocopyPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFASVGS
ParentalNTSSGEGSQPSRTENRDPLPNPWAPQASQSSSASSGTTSAVGGTSSGAASGTAGQSSTVPNLGPGVGASM
..SSGEG.QPSRTENRDPLPNPWAP.....SSA...TTS......SG..................V.AS.
RetrocopySSSSGEGTQPSRTENRDPLPNPWAPPPATQSSA---TTSTTTSSGSGSGTSSSSATGNTVAAANYV-ASI
ParentalFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLNNPLFAGN-PQLQEQMRQQLPT
F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSL.QNPDLAAQMMLN.P.F..N..QLQEQMR.QLP.
RetrocopyFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLTQNPDLAAQMMLNSPVFTAN<SQLQEQMRPQLPA
ParentalFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLGALGSTGGSSGTSG
FLQQMQNPDTLS.MSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTPG.G..G..G...G..G
RetrocopyFLQQMQNPDTLSSMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG-VGVLGTAIGPVG

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_1475 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1475 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 20 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000148272 retrocopies
retro_btau_1087, retro_btau_188,
Canis familiaris ENSCAFG000000014351 retrocopy
retro_cfam_236,
Callithrix jacchus ENSCJAG000000036092 retrocopies
retro_cjac_3977, retro_cjac_4067,
Cavia porcellus ENSCPOG000000048491 retrocopy
retro_cpor_113,
Dasypus novemcinctus ENSDNOG000000126871 retrocopy
retro_dnov_14,
Dipodomys ordii ENSDORG000000152661 retrocopy
retro_dord_680,
Equus caballus ENSECAG000000191101 retrocopy
retro_ecab_1063,
Echinops telfairi ENSETEG000000028221 retrocopy
retro_etel_39,
Felis catus ENSFCAG000000150491 retrocopy
retro_fcat_83,
Homo sapiens ENSG000001350181 retrocopy
retro_hsap_58,
Myotis lucifugus ENSMLUG000000020362 retrocopies
retro_mluc_1774, retro_mluc_33,
Mustela putorius furoENSMPUG000000020281 retrocopy
retro_mputfur_55,
Mus musculus ENSMUSG000000053121 retrocopy
retro_mmus_83,
Nomascus leucogenys ENSNLEG000000033061 retrocopy
retro_nleu_31,
Otolemur garnettii ENSOGAG000000129471 retrocopy
retro_ogar_276,
Pongo abelii ENSPPYG000000193231 retrocopy
retro_pabe_87,
Pan troglodytes ENSPTRG000000210551 retrocopy
retro_ptro_93,
Rattus norvegicus ENSRNOG000000192821 retrocopy
retro_rnor_339,
Ictidomys tridecemlineatus ENSSTOG000000134621 retrocopy
retro_itri_157,
Tursiops truncatus ENSTTRG00000004696 1 retrocopy
retro_ttru_1475 ,


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