RetrogeneDB ID:

retro_ptro_2838

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:9:78045572..78046025(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHCHD2
Ensembl ID:ENSPTRG00000019209
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2838
ATGCCGCGTGGAAGCCGAAGCCGCACCTCCCGCATGGCCCCTCCGGCCAGCCGGGCCCCTCAGATGAGAGCTGAACCCAG
GCCAGCACCAGTTGCTCAGCCACCAGCAGCGGCACCCCCATCTGCAGTTGGCTCTTCTGCTGCTGCGCCCCGGCAGCCAG
GTCTGATGGCCCAGATGGCAACCACTGCAGCTGGCGTGGCTGTGGGCTCTGCTGTGGGGCACACACAGGGTCACGCCGTT
ACTGGGGGCTTCAGTGGAGGAAGTAATGCTGAGCCTGCGAGGCCTGACATCGCTTACCAGGAGCCTCAGGGAACCCAGCC
GGCACAGCAGCAGCAGCCTTGCTTCTATGAGATCAAACAGTTTCTGGAGTGTGCCCAGAACCAGGGTGACATCAAGCTCT
GTGAGGATTTCAGTAAGGTGCTAAAACAGTGCCGACTTGCAAAATGATTGGCC

ORF - retro_ptro_2838 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.38 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPRGSRSRTSRMAPPASRAPQMRAAPRPAPVAQPPAAAPPSAVGSSAAAPRQPGLMAQMATTAAGVAVGS
MPRGSRSRTSRMAPPASRAPQMRA.PRPAPVAQPPAAAPPSAVGSSAAAPRQPGLMAQMATTAAGVAVGS
RetrocopyMPRGSRSRTSRMAPPASRAPQMRAEPRPAPVAQPPAAAPPSAVGSSAAAPRQPGLMAQMATTAAGVAVGS
ParentalAVGHTLGHAITGGFSGGSNAEPARPDITYQEPQGTQPAQQQQPCLYEIKQFLECAQNQGDIKLCEGFNEV
AVGHT.GHA.TGGFSGGSNAEPARPDI.YQEPQGTQPAQQQQPC.YEIKQFLECAQNQGDIKLCE.F..V
RetrocopyAVGHTQGHAVTGGFSGGSNAEPARPDIAYQEPQGTQPAQQQQPCFYEIKQFLECAQNQGDIKLCEDFSKV
ParentalLKQCRLANGLA
LKQCRLA..LA
RetrocopyLKQCRLAK*LA

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 .29 RPM 100 .08 RPM
SRP007412_cerebellum 0 .00 RPM 30 .61 RPM
SRP007412_heart 0 .00 RPM 43 .69 RPM
SRP007412_kidney 0 .00 RPM 112 .16 RPM
SRP007412_liver 0 .00 RPM 46 .25 RPM
SRP007412_testis 0 .00 RPM 8 .33 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2838 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2838 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2838 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4184
Gorilla gorilla retro_ggor_2807
Pongo abelii retro_pabe_139

Parental genes homology:
Parental genes homology involve 19 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160502 retrocopies
Bos taurus ENSBTAG000000402952 retrocopies
Canis familiaris ENSCAFG000000101781 retrocopy
Callithrix jacchus ENSCJAG000000212671 retrocopy
Erinaceus europaeus ENSEEUG000000128571 retrocopy
Echinops telfairi ENSETEG000000085981 retrocopy
Homo sapiens ENSG000001061538 retrocopies
Gorilla gorilla ENSGGOG000000149388 retrocopies
Myotis lucifugus ENSMLUG000000151511 retrocopy
Mus musculus ENSMUSG000000704932 retrocopies
Nomascus leucogenys ENSNLEG000000158196 retrocopies
Otolemur garnettii ENSOGAG000000100975 retrocopies
Pongo abelii ENSPPYG000000175434 retrocopies
Pan troglodytes ENSPTRG00000019209 9 retrocopies
Sus scrofa ENSSSCG000000077431 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000105123 retrocopies
Tupaia belangeri ENSTBEG0000001290515 retrocopies
Tursiops truncatus ENSTTRG000000151851 retrocopy
Vicugna pacos ENSVPAG000000061041 retrocopy



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