RetrogeneDB ID:

retro_cjac_1878

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:195732204..195732585(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5G1
Ensembl ID:ENSCJAG00000007352
Aliases:None
Description:ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) [Source:HGNC Symbol;Acc:841]


Retrocopy-Parental alignment summary:






>retro_cjac_1878
TGCTACAGGGGACAGCTGCTGAGCCGTCCACTATCTACAGTTTTTCTGAAAAGACCAGAGACACTGACAGATGAGAGTCC
CAGCAGATTGGCAGTCTCACGTCCCCTTACCTCATTTGTCTCTAGCCGCAGCTTCCAAACCAGCGCCATTTCAAGGGACA
TCGACACAGCAGCCAAGTTCATTAGTGCTGGGGCTGCCACAGTTGGGGTGGCCGGCTCTGGGGCTGGGATTGGGACTGTG
TTTGGGAGCGTCATCATTGGTTATGCCAGGAACCCTTCTCTGAAGCAACAGCTCTTCTCCTACGCCATTCTGGGCTTTGC
CCTCTCGGAGGCCATGGGGCTCTTTTGCCTGATGGTGGCCTTTCTCATCCTCTTCGCCATG

ORF - retro_cjac_1878 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.59 %
Parental protein coverage: 88.49 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalCTRG--LIRPVSASFLNSPENSSKQECSPSSSSSPLQ--VARREFQTSVVSRDIDTAAKFIGAGAATVGV
C.RG..L.RP.S..FL..PE.......S....S.PL...V..R.FQTS..SRDIDTAAKFI.AGAATVGV
RetrocopyCYRGQLLSRPLSTVFLKRPETLTDESPSRLAVSRPLTSFVSSRSFQTSAISRDIDTAAKFISAGAATVGV
ParentalAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
AGSGAGIGTVFGS.IIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
RetrocopyAGSGAGIGTVFGSVIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM

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
SRP051959_colon 0 .11 RPM 10 .05 RPM
SRP051959_heart 0 .05 RPM 18 .93 RPM
SRP051959_kidney 0 .13 RPM 11 .94 RPM
SRP051959_liver 0 .11 RPM 11 .74 RPM
SRP051959_lung 0 .05 RPM 4 .07 RPM
SRP051959_lymph_node 0 .02 RPM 3 .79 RPM
SRP051959_skeletal_muscle 0 .11 RPM 26 .14 RPM
SRP051959_spleen 0 .11 RPM 4 .08 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1878 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1878 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1878 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 27 parental genes, and 100 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000063411 retrocopy
Bos taurus ENSBTAG000000183393 retrocopies
Canis familiaris ENSCAFG000000168805 retrocopies
Callithrix jacchus ENSCJAG00000007352 7 retrocopies
Callithrix jacchus ENSCJAG000000082073 retrocopies
Cavia porcellus ENSCPOG000000090172 retrocopies
Equus caballus ENSECAG000000199081 retrocopy
Felis catus ENSFCAG000000023442 retrocopies
Homo sapiens ENSG000001591998 retrocopies
Gorilla gorilla ENSGGOG000000016268 retrocopies
Loxodonta africana ENSLAFG000000045372 retrocopies
Macropus eugenii ENSMEUG000000057442 retrocopies
Myotis lucifugus ENSMLUG000000117384 retrocopies
Macaca mulatta ENSMMUG000000133951 retrocopy
Mustela putorius furoENSMPUG000000153413 retrocopies
Mus musculus ENSMUSG000000060575 retrocopies
Nomascus leucogenys ENSNLEG000000027186 retrocopies
Oryctolagus cuniculus ENSOCUG000000162252 retrocopies
Otolemur garnettii ENSOGAG000000117133 retrocopies
Pongo abelii ENSPPYG000000089099 retrocopies
Pan troglodytes ENSPTRG000000093648 retrocopies
Rattus norvegicus ENSRNOG000000072355 retrocopies
Sus scrofa ENSSSCG000000175441 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000134042 retrocopies
Tupaia belangeri ENSTBEG000000035755 retrocopies
Tursiops truncatus ENSTTRG000000085261 retrocopy
Vicugna pacos ENSVPAG000000076531 retrocopy



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