RetrogeneDB ID:

retro_btau_934

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:21:38262862..38263209(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PPIA
Ensembl ID:ENSBTAG00000012003
Aliases:None
Description:Peptidyl-prolyl cis-trans isomerase A [Source:UniProtKB/Swiss-Prot;Acc:P62935]


Retrocopy-Parental alignment summary:






>retro_btau_934
TTAGTCAGCCTCACCATATTTTTTCCACTCGTCATCAACATTGAGCCCCTGGACAGTGTCTCCTTTGAGCTTTTTGAATA
CAGAGTTCCAAAGACAGGAGAAATTTTTTATGCTTTTAGCACTGGGAGTGAAGGTTATAAAGATTCCTGCTTTCACAGAA
GTATTCTGGGCTTTATATGCTAGGCTGAATACTTCCTATTCCATAATGACACTGGCTGCAAGTCCATATAGGAGAAACGT
TTGATGATCACAGATTCATCTTGAAGCATACTCCTGGTATCTTGTCCATGCCAAATTCTAAGCCCAACACAAACAGTTCC
TACTTTTTTATTGACATTGTCAAGACT

ORF - retro_btau_934 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.17 %
Parental protein coverage: 72.56 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRH
.V..T.FF......EPL..VSFELF...VPKT.E.F.A.STG....GYK.SCFHR.I.GF.C....F..H
RetrocopyLVSLTIFFPLVINIEPLDSVSFELFEYRVPKTGEIFYAFSTGSE--GYKDSCFHRSILGFIC*AEYFLFH
ParentalNGTGGKSI-YGEKFDDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT
N.TG.KSI..GE.FDD..FILKHT.PGILSM.N..PNTN.S.FFI...KT
RetrocopyNDTGCKSI<IGETFDDHRFILKHT-PGILSMPNSKPNTNSSYFFIDIVKT

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 0 .00 RPM 201 .58 RPM
ERP005899_muscle 0 .00 RPM 239 .93 RPM
SRP017611_brain 0 .00 RPM 254 .98 RPM
SRP017611_kidney 0 .00 RPM 275 .02 RPM
SRP017611_liver 0 .00 RPM 137 .12 RPM
SRP030211_testis 0 .03 RPM 219 .45 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_934 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_934 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_934 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 464 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000012003 12 retrocopies
Callithrix jacchus ENSCJAG0000001196954 retrocopies
Cavia porcellus ENSCPOG0000000263211 retrocopies
Echinops telfairi ENSETEG0000000218621 retrocopies
Homo sapiens ENSG0000019626278 retrocopies
Gorilla gorilla ENSGGOG000000262984 retrocopies
Loxodonta africana ENSLAFG000000113451 retrocopy
Macropus eugenii ENSMEUG0000000201620 retrocopies
Macaca mulatta ENSMMUG0000001663810 retrocopies
Monodelphis domestica ENSMODG000000160899 retrocopies
Mus musculus ENSMUSG000000718662 retrocopies
Oryctolagus cuniculus ENSOCUG000000166623 retrocopies
Otolemur garnettii ENSOGAG0000002799731 retrocopies
Pongo abelii ENSPPYG0000001758612 retrocopies
Pongo abelii ENSPPYG000000175874 retrocopies
Pan troglodytes ENSPTRG0000002306477 retrocopies
Rattus norvegicus ENSRNOG000000064232 retrocopies
Sarcophilus harrisii ENSSHAG000000170623 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001021510 retrocopies
Tupaia belangeri ENSTBEG0000001748477 retrocopies
Tarsius syrichta ENSTSYG0000000897323 retrocopies



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