RetrogeneDB ID:

retro_cjac_505

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:15784878..15785129(-)
Located in intron of:ENSCJAG00000021012
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:COX5B
Ensembl ID:ENSCJAG00000016911
Aliases:None
Description:cytochrome c oxidase subunit Vb [Source:HGNC Symbol;Acc:2269]


Retrocopy-Parental alignment summary:






>retro_cjac_505
ACTGGCTTGGAGAGGGAGGTCATGATGGCTGCAAGGAAGGGACTGGACCCACACGAGGTACTACTCCCAAAGGCAGCTTC
AGGTACCAAGGAAGACCCTAATTTAGTCCCTTCAATCACCAACAAGAGAATAGTGGTGTACCTGAAGAGGACAACAGTGC
CGTCATCTGGTTTGGGCTGCACAAAGGCAAGAGCCAGCAGTGCCTCAGCTGTGGAACCCATTACAAGCTGGTGCCCCACC
AGCTGGCACAC

ORF - retro_cjac_505 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.09 %
Parental protein coverage: 89.47 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTGLEREIMLAARKGLDPYNILPPKGASGTKEDPNLVPSVTNKRIV-GCICEEDNSTVIWFWLHKGEAQRC
TGLERE.M.AARKGLDP...L.PK.ASGTKEDPNLVPS.TNKRIV.G...E.....VIWF.LHKG..Q.C
RetrocopyTGLEREVMMAARKGLDPHEVLLPKAASGTKEDPNLVPSITNKRIV<GVPEEDNSA-VIWFGLHKGKSQQC
ParentalPSCGAYYKLVPHQLAH
.SCG..YKLVPHQLAH
RetrocopyLSCGTHYKLVPHQLAH

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 .33 RPM 23 .36 RPM
SRP051959_heart 0 .25 RPM 73 .63 RPM
SRP051959_kidney 0 .49 RPM 33 .61 RPM
SRP051959_liver 0 .32 RPM 27 .47 RPM
SRP051959_lung 0 .33 RPM 13 .14 RPM
SRP051959_lymph_node 0 .50 RPM 17 .94 RPM
SRP051959_skeletal_muscle 0 .00 RPM 87 .07 RPM
SRP051959_spleen 1 .30 RPM 17 .69 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_505 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_505 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_505 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 29 parental genes, and 113 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000052427 retrocopies
Bos taurus ENSBTAG000000185422 retrocopies
Canis familiaris ENSCAFG000000023878 retrocopies
Callithrix jacchus ENSCJAG00000016911 6 retrocopies
Dipodomys ordii ENSDORG000000149943 retrocopies
Equus caballus ENSECAG000000079683 retrocopies
Erinaceus europaeus ENSEEUG000000002581 retrocopy
Felis catus ENSFCAG000000017047 retrocopies
Homo sapiens ENSG000001359407 retrocopies
Gorilla gorilla ENSGGOG000000011426 retrocopies
Loxodonta africana ENSLAFG000000093862 retrocopies
Macropus eugenii ENSMEUG000000058552 retrocopies
Myotis lucifugus ENSMLUG000000145121 retrocopy
Mustela putorius furoENSMPUG000000113278 retrocopies
Mus musculus ENSMUSG000000615181 retrocopy
Nomascus leucogenys ENSNLEG000000116685 retrocopies
Oryctolagus cuniculus ENSOCUG000000170852 retrocopies
Otolemur garnettii ENSOGAG000000168403 retrocopies
Ochotona princeps ENSOPRG000000020303 retrocopies
Pongo abelii ENSPPYG000000120786 retrocopies
Pan troglodytes ENSPTRG000000122577 retrocopies
Rattus norvegicus ENSRNOG000000166602 retrocopies
Sorex araneus ENSSARG000000112751 retrocopy
Sarcophilus harrisii ENSSHAG000000173583 retrocopies
Sus scrofa ENSSSCG000000081954 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000109803 retrocopies
Tupaia belangeri ENSTBEG000000121304 retrocopies
Tursiops truncatus ENSTTRG000000134905 retrocopies
Vicugna pacos ENSVPAG000000065601 retrocopy



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