RetrogeneDB ID:

retro_ttru_79

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:GeneScaffold_116:140148..140427(-)
Located in intron of:ENSTTRG00000012860
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HIGD1A
Ensembl ID:ENSTTRG00000009760
Aliases:None
Description:HIG1 hypoxia inducible domain family, member 1A [Source:HGNC Symbol;Acc:29527]


Retrocopy-Parental alignment summary:






>retro_ttru_79
ATGTCAAGTGACACAGATGTTTCTCTTTCTTCATATGGTGAAGATTAGGGATCTAAATTTACCCTAAAAGCTAGAGAGGC
ACCATTTGTCCGCATTGGAATGGCAGGTTTTGCAGCAATCGTTGCATATGGATTATATAAATTGAAGAACAGGGGCAATA
CTAAAATGTCTGTTCACCTGATCCACATGCGTGTGGCAGCCCAAGGCTTTGTTGTGGGAGCAGTGACTCTTGGTATGGGC
TATTCCATGTATCAAGAAATCTGGGCAGAACCTAAACCT

ORF - retro_ttru_79 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.1 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSSDTDVSLSSYDEGQGSKLIRKAREAPFVPIGMAGFAAIVAYGLYKLKSRGNTKMSV-LIHMRVAAQGF
MSSDTDVSLSSY.E..GSK...KAREAPFV.IGMAGFAAIVAYGLYKLK.RGNTKMSV.LIHMRVAAQGF
RetrocopyMSSDTDVSLSSYGED*GSKFTLKAREAPFVRIGMAGFAAIVAYGLYKLKNRGNTKMSVHLIHMRVAAQGF
ParentalVVGAMTLGMGYSMYQEFWAKPKP
VVGA.TLGMGYSMYQE.WA.PKP
RetrocopyVVGAVTLGMGYSMYQEIWAEPKP

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






Tursiops truncatus was not studied using RNA-Seq expression data.
Tursiops truncatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ttru_79 retrocopy.
Tursiops truncatus was not studied using FANTOM5 data.
retro_ttru_79 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 22 parental genes, and 114 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000124311 retrocopy
Choloepus hoffmanni ENSCHOG0000000907910 retrocopies
Callithrix jacchus ENSCJAG000000326689 retrocopies
Cavia porcellus ENSCPOG0000000070311 retrocopies
Equus caballus ENSECAG000000109781 retrocopy
Echinops telfairi ENSETEG000000074934 retrocopies
Felis catus ENSFCAG000000005372 retrocopies
Homo sapiens ENSG0000018106113 retrocopies
Gorilla gorilla ENSGGOG000000167593 retrocopies
Macaca mulatta ENSMMUG0000001878311 retrocopies
Monodelphis domestica ENSMODG000000136056 retrocopies
Mustela putorius furoENSMPUG000000118703 retrocopies
Mus musculus ENSMUSG000000384121 retrocopy
Otolemur garnettii ENSOGAG000000113583 retrocopies
Ochotona princeps ENSOPRG000000160721 retrocopy
Pongo abelii ENSPPYG0000001397416 retrocopies
Pan troglodytes ENSPTRG000000148021 retrocopy
Rattus norvegicus ENSRNOG000000194281 retrocopy
Sus scrofa ENSSSCG000000112901 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000096813 retrocopies
Tupaia belangeri ENSTBEG000000023245 retrocopies
Tursiops truncatus ENSTTRG00000009760 8 retrocopies



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