RetrogeneDB ID:

retro_ptro_1100

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:16:45120285..45120600(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RARRES2
Ensembl ID:ENSPTRG00000019854
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1100
CACCCGCCTGTGCAGTGGCCTTCTGGGAGACCAGTGTGTACGGCACCATGGACACGGCCTTCCCAGCTGGAACATTTGTG
AGGCTGTAATTTAAGCTCAGGCATACAAGCGGCCAGAAGGTGGACTGGATGCAATCTGAGCGCAAAGTCCAACCTAGGGG
GAGTAAGCGGAAATGCCTGGCCTGCGTCAAACTGGGCTCTTAGGATAAGGTTCTAGGCTAGATGGCCACTGCCTTATAGA
GACGCAGGTTCGGCGGGAGCCTGAGGAGCACCAGGGACCCAGTGCACCAGGGCGCAGTGGGCAGCGACAGCCCCA

ORF - retro_ptro_1100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.14 %
Parental protein coverage: 65.03 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalHPPVQW-AFQETSVESAVDTPFPAGIFVRLEFKLQQTSCRKRDWKKPECKVRPNGRKRKCLACIKLGSED
HPPVQW.AF.ETSV....DT.FPAG.FVRL.FKL..TS..K.DW...E.KV.P.G.KRKCLAC.KLGS.D
RetrocopyHPPVQW<AFWETSVYGTMDTAFPAGTFVRL*FKLRHTSGQKVDWMQSERKVQPRGSKRKCLACVKLGS*D
ParentalKVLGRLV-HCPIETQVLREAEEHQ-ETQCLRVQQAGEDP
KVLG....HC.IETQV.RE.EEHQ..TQC.R.Q.A...P
RetrocopyKVLG*MA<HCLIETQVRREPEEHQ<GTQCTRAQWAATAP

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 .00 RPM 8 .65 RPM
SRP007412_cerebellum 0 .00 RPM 12 .30 RPM
SRP007412_heart 0 .00 RPM 4 .05 RPM
SRP007412_kidney 0 .00 RPM 119 .75 RPM
SRP007412_liver 0 .03 RPM 623 .85 RPM
SRP007412_testis 0 .00 RPM 4 .22 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1100 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1100 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1100 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1678

Parental genes homology:
Parental genes homology involve 7 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000103225 retrocopies
Homo sapiens ENSG0000010653813 retrocopies
Gorilla gorilla ENSGGOG000000111581 retrocopy
Macaca mulatta ENSMMUG000000052324 retrocopies
Nomascus leucogenys ENSNLEG0000000136218 retrocopies
Pongo abelii ENSPPYG0000001816628 retrocopies
Pan troglodytes ENSPTRG00000019854 10 retrocopies



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