RetrogeneDB ID:

retro_ptro_1001

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:15:32104092..32104323(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NUTF2
Ensembl ID:ENSPTRG00000008248
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1001
ATGGGAGACGAGCCAATCTGGGAGCAGATTGGATCCAGCTTCATTCAGCATTACTACCAGTTATTTCATAATGATAAAAC
CCAACTAGGTGCAATTTACATTGATGTGCCATGCCTTACGTGGGAAGGACAGCAGTTCCAGGGGAAAGCTGCCATTGTGG
AGAAGTTGTCTAGTCATCCCTTCCAAAAAATCCAGCACAGCATCACAGCACAGGACCATCAGCCCATGCCA

ORF - retro_ptro_1001 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.91 %
Parental protein coverage: 60.63 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITA
MGD.PIWEQIGSSFIQHYYQLF.ND.TQLGAIYID..CLTWEGQQFQGKAAIVEKLSS.PFQKIQHSITA
RetrocopyMGDEPIWEQIGSSFIQHYYQLFHNDKTQLGAIYIDVPCLTWEGQQFQGKAAIVEKLSSHPFQKIQHSITA
ParentalQDHQPTP
QDHQP.P
RetrocopyQDHQPMP

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
SRP007412_brain_prefrontal_cortex 0 .11 RPM 65 .22 RPM
SRP007412_cerebellum 0 .00 RPM 27 .07 RPM
SRP007412_heart 0 .00 RPM 18 .04 RPM
SRP007412_kidney 0 .08 RPM 30 .55 RPM
SRP007412_liver 0 .00 RPM 19 .21 RPM
SRP007412_testis 0 .00 RPM 19 .50 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1001 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1001 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1001 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1480
Pongo abelii retro_pabe_1229
Macaca mulatta retro_mmul_2127

Parental genes homology:
Parental genes homology involve 24 parental genes, and 103 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000175485 retrocopies
Choloepus hoffmanni ENSCHOG000000030593 retrocopies
Callithrix jacchus ENSCJAG0000001601514 retrocopies
Equus caballus ENSECAG000000215301 retrocopy
Felis catus ENSFCAG000000081673 retrocopies
Homo sapiens ENSG000001028987 retrocopies
Gorilla gorilla ENSGGOG000000239255 retrocopies
Loxodonta africana ENSLAFG000000310371 retrocopy
Macropus eugenii ENSMEUG0000000987411 retrocopies
Myotis lucifugus ENSMLUG000000251753 retrocopies
Macaca mulatta ENSMMUG000000120386 retrocopies
Monodelphis domestica ENSMODG000000055176 retrocopies
Mustela putorius furoENSMPUG000000067374 retrocopies
Mus musculus ENSMUSG000000084501 retrocopy
Nomascus leucogenys ENSNLEG000000048897 retrocopies
Oryctolagus cuniculus ENSOCUG000000063221 retrocopy
Ochotona princeps ENSOPRG000000137274 retrocopies
Procavia capensis ENSPCAG000000153441 retrocopy
Pongo abelii ENSPPYG000000074727 retrocopies
Pan troglodytes ENSPTRG00000008248 7 retrocopies
Pteropus vampyrus ENSPVAG000000166051 retrocopy
Sarcophilus harrisii ENSSHAG000000061001 retrocopy
Sus scrofa ENSSSCG000000302953 retrocopies
Drosophila melanogaster FBgn00311451 retrocopy



Copyright © RetrogeneDB 2014-2017