RetrogeneDB ID:

retro_cjac_1860

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:160093740..160093974(+)
Located in intron of:ENSCJAG00000001300
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TOMM20
Ensembl ID:ENSCJAG00000018127
Aliases:None
Description:translocase of outer mitochondrial membrane 20 homolog (yeast) [Source:HGNC Symbol;Acc:20947]


Retrocopy-Parental alignment summary:






>retro_cjac_1860
AAAGAAAGAAACAGACAGAAGCTTGCCAAGGAGAGAGCTGGGCTTTCCAAGTTACCTGACCTTAAAGATGCTGAAGCTGT
TCAGAAATTCTTCCTTGAAGAAATACAACTTGGTGAAGAATTACTAGCCCAAGGTGAATATGAGAAGGAAGTAGACCATC
TGACGAATGCAACTGCTGTGTGTGGACAGCCACAGCAGTTACTTACAGCAAACTCTTCCACCACCAGTGTTCCA

ORF - retro_cjac_1860 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.05 %
Parental protein coverage: 53.79 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalERRKKQKLAKERAGLSKLPDLKDAEAVQKFFLEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQV
..R..QKLAKERAGLSKLPDLKDAEAVQKFFLEEIQLGEELLAQGEYEK.VDHLTNA.AVCGQPQQLL..
RetrocopyKERNRQKLAKERAGLSKLPDLKDAEAVQKFFLEEIQLGEELLAQGEYEKEVDHLTNATAVCGQPQQLLTA
ParentalLQQTLPPP
...T...P
RetrocopyNSSTTSVP

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 .02 RPM 23 .70 RPM
SRP051959_heart 0 .07 RPM 25 .73 RPM
SRP051959_kidney 0 .00 RPM 23 .25 RPM
SRP051959_liver 0 .06 RPM 34 .83 RPM
SRP051959_lung 0 .03 RPM 17 .67 RPM
SRP051959_lymph_node 0 .00 RPM 13 .36 RPM
SRP051959_skeletal_muscle 0 .00 RPM 25 .90 RPM
SRP051959_spleen 0 .02 RPM 18 .68 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1860 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1860 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1860 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 18 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000005625 retrocopies
Choloepus hoffmanni ENSCHOG000000023837 retrocopies
Callithrix jacchus ENSCJAG00000018127 3 retrocopies
retro_cjac_1860 , retro_cjac_2420, retro_cjac_918,
Echinops telfairi ENSETEG000000176934 retrocopies
Homo sapiens ENSG000001737265 retrocopies
Gorilla gorilla ENSGGOG000000251845 retrocopies
Loxodonta africana ENSLAFG000000154991 retrocopy
Myotis lucifugus ENSMLUG000000162181 retrocopy
Macaca mulatta ENSMMUG000000071362 retrocopies
Monodelphis domestica ENSMODG000000084526 retrocopies
Mus musculus ENSMUSG0000009390412 retrocopies
Pongo abelii ENSPPYG000000000994 retrocopies
Pan troglodytes ENSPTRG000000021275 retrocopies
Rattus norvegicus ENSRNOG000000199804 retrocopies
Sarcophilus harrisii ENSSHAG000000158763 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000275643 retrocopies
Tupaia belangeri ENSTBEG0000000382726 retrocopies
Vicugna pacos ENSVPAG000000039801 retrocopy



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