RetrogeneDB ID:

retro_ttru_1401

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_112419:4746..5965(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAD23B
Ensembl ID:ENSTTRG00000007597
Aliases:None
Description:RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]


Retrocopy-Parental alignment summary:






>retro_ttru_1401
ATGCTGGTCACCCTGGAGACCGTCCAGCAGCAGATCTTCAAGATCGACATCGACCCAAACGAGATGGTAAGAGCACTGAA
TGAGAAGACTGAATCTGAAAAGGGTAAAGATGCCTTTCCTGTAGCAGGTCAAAAATTAATTTAGCAGGCAAAATTCTCAA
TAATGATACTGCTCTAAAAGAATATAAAATTGACGAGAAAAACTTCGTGGTAGTTATGGTGAGAAGACCCAAAGCAGTGA
CACCACCAGCACCAGCTACAACTTAGCAATCTAATTCTGCCACCACTACCACAGTTAGTTCCTCCACAGCACCAGCTGTG
GCTCAGGCCCCAACCCCTGCCCTCACTTTGGCCCCCACTCCCACACCTGCATCTGTCACTCCAGCATCAACGACAGCATC
TTCTGAACCTGCACCTGCTAGTGCAATGAAACAAGAAAAACCTGCAGAAAAGCCAGCAGAAACACCAGTGGCTGCTAGCC
CAACATCAACTGACAGTACATCAGGTGATTCTTCTTGGTCAAACCTTTTTGAAGATGCAACAAGTGCCCTTGTGACAAGT
CAGTCTTAGGAGAATATGGTAACTGAGATCATGTCAATGGGCTATGAACGGCAGCAAGTAATCGCAGCACTGAGAGCCAG
TTTCAACAACCCTGACAGCAGTGGAGTATTTTTTAATGGGAATTCCCAGAGATAGAGAAAGTCAGGCCGTGGTTGACTCC
CCTCCAGCAGCGAGTAGTGGGGCTCCTCAGTCTTCAGTGGCTGCAGCTGCAGCAACTACGACAGCAACAACTACAACAAG
TTCTGGAGCACACCCTCTTGCATTTTTACGGAATCAGCCTCAGTTTCAACAGAGGAGACAAATTATTCAACAGAATCCTT
CCCTGCTTCCAGCATCGCTACAACAGATAGGTCGAGAAAATCCTCAGTTACTGCAGCAAATTAGCCACCATCAGGAGCAT
TTTATTCAGATGTTATATTGAACCAGTTCAAGAAGTGGGGGGTCAAGGAGGAGGGGGTGGAAGTGGCAGTGGAGGAATTG
CAGAAGCTGGAAGTGGTCATATGAACTACATTCAAATAACGCCTCAGGAAGAAGAAGCTATAGAAAGGTTAAAGGCATTA
GGATTTCCTGAAGGACTTGTGATACAAGCATATTTTGCTTGTGAGAGGAATGAGAACTTGGCTGCCAATTTTCCTGTACA
GCAAAACTTTGATGAAGAT

ORF - retro_ttru_1401 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.99 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMLVTL-TLQQQTFXXXXXXXXXVRALKEKIESEKGKDAFPVAGQKLI-YAGKILNDDTALKEYKIDEKNF
MLVTL.T.QQQ.F.........VRAL.EK.ESEKGKDAFPVAGQKLI..AGKILN.DTALKEYKIDEKNF
RetrocopyMLVTLETVQQQIFKIDIDPNEMVRALNEKTESEKGKDAFPVAGQKLI<LAGKILNNDTALKEYKIDEKNF
ParentalVVVMVTKPKAVTTPAPATTQQSNSATTTTVSSSTAPTVVQAPTPAPTLAPAPAPTPASVTPASTTASSEP
VVVMV..PKAVT.PAPATT.QSNSATTTTVSSSTAP.V.QAPTPA.TLAP.P..TPASVTPASTTASSEP
RetrocopyVVVMVRRPKAVTPPAPATT*QSNSATTTTVSSSTAPAVAQAPTPALTLAPTP--TPASVTPASTTASSEP
ParentalAPASATKQEKPAEKPAETPVAASPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQV
APASA.KQEKPAEKPAETPVAASPTSTDSTSGDSS.SNLFEDATSALVT.QS.ENMVTEIMSMGYER.QV
RetrocopyAPASAMKQEKPAEKPAETPVAASPTSTDSTSGDSSWSNLFEDATSALVTSQS*ENMVTEIMSMGYERQQV
ParentalIAALRAS-FNNPDR-AVEYLLMGIPGDRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSGGHPL
IAALRAS.F..P...AVEY.LMGIP.DRESQAVVD.PPAAS.GAPQSSVAAAAATTTATTTT.SSG.HPL
RetrocopyIAALRAS<FQQP*Q<AVEYFLMGIPRDRESQAVVDSPPAASSGAPQSSVAAAAATTTATTTT-SSGAHPL
ParentalEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLN-EPVQEAGGQGGGSGGG
.FLRNQPQFQQ.RQIIQQNPSLLPA.LQQIGRENPQLLQQIS.HQEHFIQML..EPVQE.GGQGGG.G.G
RetrocopyAFLRNQPQFQQRRQIIQQNPSLLPASLQQIGRENPQLLQQISHHQEHFIQMLY>EPVQEVGGQGGGGGSG
ParentalSGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
SGGIAEAGSGHMNYIQ.TPQE.EAIERLKALGFPEGLVIQAYFACE.NENLAANF..QQNFDED
RetrocopySGGIAEAGSGHMNYIQITPQEEEAIERLKALGFPEGLVIQAYFACERNENLAANFPVQQNFDED

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_1401 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1401 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 16 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000019261 retrocopy
retro_btau_877,
Callithrix jacchus ENSCJAG000000169082 retrocopies
retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus ENSDNOG000000011742 retrocopies
retro_dnov_1982, retro_dnov_989,
Equus caballus ENSECAG000000219281 retrocopy
retro_ecab_361,
Homo sapiens ENSG000001193182 retrocopies
retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla ENSGGOG000000025111 retrocopy
retro_ggor_1829,
Loxodonta africana ENSLAFG000000075331 retrocopy
retro_lafr_1109,
Macaca mulatta ENSMMUG000000149442 retrocopies
retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys ENSNLEG000000173191 retrocopy
retro_nleu_1590,
Oryctolagus cuniculus ENSOCUG000000073161 retrocopy
retro_ocun_1429,
Otolemur garnettii ENSOGAG000000142161 retrocopy
retro_ogar_3040,
Pongo abelii ENSPPYG000000194772 retrocopies
retro_pabe_2344, retro_pabe_3162,
Pan troglodytes ENSPTRG000000212291 retrocopy
retro_ptro_1760,
Sarcophilus harrisii ENSSHAG000000119251 retrocopy
retro_shar_248,
Sus scrofa ENSSSCG000000054361 retrocopy
retro_sscr_770,
Tursiops truncatus ENSTTRG00000007597 1 retrocopy
retro_ttru_1401 ,


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