RetrogeneDB ID:

retro_ptro_2117

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:4:186817083..186817332(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TOMM22
Ensembl ID:ENSPTRG00000014374
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2117
TGGCGCCAAATGGAGATGCTCCCAAAGAACTCTGGTCTGTAGCTGGATCCATTTCTGATCTCTCCCTCTTCATGGCTCAA
AAGATATACGGATTTTCCAGAACAGCCTTGTGGATTGCAACCACTTTCTTTATACTCCTGGCTGTTCTGTTGTCTTGGAG
ACTAAGTCACAAGTGGAACAACAGCAGCAACTAGAAGCAGCAGTGGATACTTTCTAGGGCCTACCACGGGGCCTACCACA
GGCTCTCCC

ORF - retro_ptro_2117 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.68 %
Parental protein coverage: 59.15 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalWGLTEMFPER-VRSAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVL-PVVFETEKLQMEQQQQLQ-
W...EM.P.....S.AG...DLSLF.AQK.Y.FSR.ALWI.TT.F..L....VV.ET.K.Q.EQQQQL..
RetrocopyWRQMEMLPKN<LWSVAGSISDLSLFMAQKIYGFSRTALWIATTFFILLAV<SVVLET-KSQVEQQQQLE>
ParentalQRQIL-LGPNTGLSGGMP
Q..IL.LGP.TG...G.P
RetrocopyQQWIL>LGPTTGPTTGSP

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 .04 RPM 36 .50 RPM
SRP007412_cerebellum 0 .04 RPM 19 .39 RPM
SRP007412_heart 0 .00 RPM 22 .27 RPM
SRP007412_kidney 0 .03 RPM 30 .05 RPM
SRP007412_liver 0 .10 RPM 27 .17 RPM
SRP007412_testis 0 .11 RPM 54 .06 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2117 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2117 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2117 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 85 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000106923 retrocopies
Canis familiaris ENSCAFG000000013832 retrocopies
Callithrix jacchus ENSCJAG000000117315 retrocopies
Cavia porcellus ENSCPOG000000059631 retrocopy
Equus caballus ENSECAG000000103591 retrocopy
Erinaceus europaeus ENSEEUG000000064281 retrocopy
Echinops telfairi ENSETEG000000005447 retrocopies
Homo sapiens ENSG000001002166 retrocopies
Gorilla gorilla ENSGGOG000000132304 retrocopies
Macropus eugenii ENSMEUG000000029011 retrocopy
Microcebus murinus ENSMICG000000117923 retrocopies
Myotis lucifugus ENSMLUG000000037612 retrocopies
Macaca mulatta ENSMMUG000000003648 retrocopies
Mustela putorius furoENSMPUG000000131562 retrocopies
Mus musculus ENSMUSG000000224272 retrocopies
Nomascus leucogenys ENSNLEG000000151596 retrocopies
Otolemur garnettii ENSOGAG000000295839 retrocopies
Pongo abelii ENSPPYG000000118256 retrocopies
Pan troglodytes ENSPTRG00000014374 6 retrocopies
Rattus norvegicus ENSRNOG000000140584 retrocopies
Sus scrofa ENSSSCG000000000971 retrocopy
Tupaia belangeri ENSTBEG000000156834 retrocopies
Vicugna pacos ENSVPAG000000014851 retrocopy



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