RetrogeneDB ID:

retro_ptro_2203

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:156258055..156258918(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:OBFC1
Ensembl ID:ENSPTRG00000002919
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2203
ACTGGAGTTATAAACTGCATCTGCTAGAAAATATTGAGCAATATCAAGTTTTCATCCACTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGACACCGTTGAGCAGAGAACAAAAATTGAAACTGGGGACATGTTCT
GAATCAGAGGCTATGTCTACACGTGCAGAGAAGAGTGAGAAATTTATGCCACTGCTTATTATAAAGTGGACGATCCAGTG
TGGAACATTCAAATTGCAAGGGTGTTTGAGCTGCCCATTAATCTACAGGGAAGTTTAGACCAAGCCTTTCCATTGCCCAG
ACTTAGAGAAAGAAGAAGCACTAAGCAATCCAGGTGTCCTGGCCTTCACTAGTCTCATGTGTTTGCTGAGTGAAAAAGCC
AAAGAATTCCCCATAAAGAACAGAGTGCAGACCTTTGACCAGCAGGAGTTGGAAATGGTGGATCCTTTGCTGTCCCTTGC
TAACCAGCCTGTTACTGACAGTGCCTGCTCTGAACAAGGAAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCA
TATTTTAAAATGCTATTCAACAGCTGCAGGAAAAAGGACTCGTTTTCCAGAAAGATGGTGGTTTTGATAACCTATGCTGT
GTAACCAGAAAAGACAAAGACCTGTATAGGAAAATCCACTGGATAATTCAGAAAGACTACCAGAAACCAAATCACCCGAA
GAAGGGCTGCCACTTCCTGCACATCTTGGCCTGCGCTCACCCTGAGCATCTGCCCAGTTCTAGTTAGGGCTATGTTGCAG
CAAGTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAGCACAATGGAGCACCACTACTCC

ORF - retro_ptro_2203 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.01 %
Parental protein coverage: 77.72 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIEQRTKIEIGDTIRVRGSIRTYREEREIHA
TGVINCIC.K.L.N....S.AP.AARELS.TS.LKKLQ.T.EQRTKIE.GD....RG...T.REE.EI.A
RetrocopyTGVINCIC*KILSNIKFSSTAPNAARELSFTSILKKLQDTVEQRTKIETGDMF*IRGYVYTCREE*EIYA
ParentalTAYYKVDDPVWNIQIARMLELPT-IYRKVYDQPFHSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLME
TAYYKVDDPVWNIQIAR..ELP..IYR.V...PFH...LEKEEALSNPG.L...SL..LLSEKAKEF...
RetrocopyTAYYKVDDPVWNIQIARVFELPI>IYREV*TKPFHCPDLEKEEALSNPGVLAFTSLMCLLSEKAKEFPIK
ParentalNRVQSFYQQELEMVESLLSLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLQEKGLVFQKDDGFD
NRVQ.F.QQELEMV..LLSLANQPV..SACS.Q.NFKKD.T.KAI.SIF.NAIQ.LQEKGLVFQKD.GFD
RetrocopyNRVQTFDQQELEMVDPLLSLANQPVTDSACSEQGNFKKDITFKAIYSIF*NAIQQLQEKGLVFQKDGGFD
ParentalNLYYVTREDKDLHRKIHRIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI
NL..VTR.DKDL.RKIH.IIQ.D.QKPNH..KGCHFLHILACA..LSI.P.L..A.LQQVLELLEDQSD.
RetrocopyNLCCVTRKDKDLYRKIHWIIQKDYQKPNHPKKGCHFLHILACAH>LSICPVLVRAMLQQVLELLEDQSDL
ParentalVSTMEHYYT
.STMEH.Y.
RetrocopyISTMEHHYS

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 .00 RPM 5 .56 RPM
SRP007412_cerebellum 0 .04 RPM 6 .13 RPM
SRP007412_heart 0 .09 RPM 13 .03 RPM
SRP007412_kidney 0 .00 RPM 16 .89 RPM
SRP007412_liver 0 .00 RPM 7 .23 RPM
SRP007412_testis 0 .00 RPM 35 .83 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2203 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2203 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2203 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3257
Gorilla gorilla retro_ggor_2219
Pongo abelii retro_pabe_2701
Macaca mulatta retro_mmul_2050
Callithrix jacchus retro_cjac_1791

Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000183421 retrocopy
Homo sapiens ENSG000001079601 retrocopy
Gorilla gorilla ENSGGOG000000089791 retrocopy
Macaca mulatta ENSMMUG000000153231 retrocopy
Nomascus leucogenys ENSNLEG000000152821 retrocopy
Pongo abelii ENSPPYG000000026281 retrocopy
Pan troglodytes ENSPTRG00000002919 1 retrocopy
retro_ptro_2203 ,



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