RetrogeneDB ID:

retro_ptro_1317

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:19:20363211..20363554(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BNIP3
Ensembl ID:ENSPTRG00000003067
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1317
AACCAACAGAGCTTCTGAAACACCCAAGGCATTGGAGAGAAAAACAGTTATTAGTCTGTGGAAGATTATATTGACAGAAA
GAAAGAAATTGAAAGCATATTGAAGGAATACTCAGATTAGATACGGGATTGGTTAAGTGAGCAAGAAAAAATTCCCCCCA
ATGTTTCTCTTTAAAGAACCAAAGTGCACAGCTACTCTCAGCATGAGAAACACACGCATTCTGAAGAACAGATACATATT
CTATCTAGAATTTCTAGAGGTTTTTCTTCCATCTTTGCTGCTGTCTCATCCGCTGGCCATTGGACTAGGGATTTATATTG
GAAGCCATCTAACAACATCCACC

ORF - retro_ptro_1317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.38 %
Parental protein coverage: 59.28 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalNRASETDTHSIGEKNSSQSEEDDIERRKEVESILKKNSDWIWDWSSRPENI-PPKEFLFKHPKRTATLSM
N..S...T..IGEKNS..S.ED.I.R.KE.ESILK..SD.I.DW.S..E.I.PP..FLFK.PK.TATLSM
RetrocopyNQQSF*NTQGIGEKNSY*SVEDYIDRKKEIESILKEYSD*IRDWLSEQEKI>PPM-FLFKEPKCTATLSM
ParentalRNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTST
RNT...K...IF..EFL.VFLPSLLLSH.LAIGLGIYIG..LTTST
RetrocopyRNTRILKNRYIFYLEFLEVFLPSLLLSHPLAIGLGIYIGSHLTTST

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 .04 RPM 98 .38 RPM
SRP007412_cerebellum 0 .00 RPM 51 .51 RPM
SRP007412_heart 0 .03 RPM 98 .51 RPM
SRP007412_kidney 0 .00 RPM 70 .09 RPM
SRP007412_liver 0 .00 RPM 53 .55 RPM
SRP007412_testis 0 .00 RPM 29 .51 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1317 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1317 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1317 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 146 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000021502 retrocopies
Callithrix jacchus ENSCJAG000000002288 retrocopies
Cavia porcellus ENSCPOG000000058827 retrocopies
Dipodomys ordii ENSDORG000000125111 retrocopy
Equus caballus ENSECAG000000174583 retrocopies
Echinops telfairi ENSETEG000000117041 retrocopy
Homo sapiens ENSG0000017617121 retrocopies
Gorilla gorilla ENSGGOG0000001452017 retrocopies
Microcebus murinus ENSMICG000000119851 retrocopy
Macaca mulatta ENSMMUG0000002244513 retrocopies
Mus musculus ENSMUSG000000785664 retrocopies
Nomascus leucogenys ENSNLEG0000000161326 retrocopies
Pongo abelii ENSPPYG0000000277118 retrocopies
Pan troglodytes ENSPTRG00000003067 17 retrocopies
Rattus norvegicus ENSRNOG000000172433 retrocopies
Sus scrofa ENSSSCG000000243881 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000124561 retrocopy
Tupaia belangeri ENSTBEG000000004871 retrocopy
Tursiops truncatus ENSTTRG000000080381 retrocopy



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