RetrogeneDB ID:

retro_pabe_3294

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:8:135173314..135174395(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000018877
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000017210
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_3294
ATGGCGGGACACCTGACTTCGGATTTCGCCTTCTCACCCCCTCCAGGCGGTGCAGGTGATGGGCCAGGGGGCCGAAGACG
GGCTGGGTTGATCCTCGGACCTGGCTAAGCTTCCAAGGCCCTCCTGGAGGGCCAGGAATAGGGCCAGGGGTTGGGCCAGG
CGCTGAGGAGCCATGGGGATTCCCCCATGCCCCCCGCCGTACGAGTTCTGTGGGGGGATGGCGTACTGTGGGCCTCAGGT
TGGAGTGGGGCTGGTGCCCCAAGGCTGCTTGGAGACCTCTCAGCCTGAGGGCGAAGCAGGAGTCCGGGTGGAGAGCAACT
CCGATGGGGCCTCCCCGGAGCCCTGCACCTTCCCCCCTGGTGCCGTGAAGCTGGAGAAGGAGAAACTGGAGCAAAACCCG
GAGGAGTCCCAGGACATCAAAGCTCTGCAGAAAGAACTCGAGCAATTTGCCAAGCTCCTGAAGCAGAAGAGGATCACCCT
GGGATATACACAGGCCGATGTGGGGCTCATCCTGGGGGTTCTATTTGGGAAGGTGTTCAGCCAAACGACCATCTGCCGCT
TTGAGGCTCTGCAGCTTAGCTTCAAGAACGTGTGTGAGCTGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAAC
AATGAAAATCTTCAGGAGATATGCAAAGCAGAAACCCTCGTGCAGGCCCGAAAGAGAAAGCGAACCAGTATCGAGAACCG
AGTGAGAGGCAACCTGGAGAATTTGTTCCTGCAGTGCCCGAAACCCACACTGCAGCAGATCAGCCACATCGCCCAGCAGC
TTGGGCTCGAGAATGATGTGGTCCGAGTGTGGTTCTGTAACCGGCGCCAGAACGGCAAGCGATCAAGCAGTGACTATGCA
CAACGAGAGCATTTTGAGGCTGCTGGGTCTCCTTTCTCAGGGGGAACCAGTGTCCTTTCCTCTGGCCCCAGGGCCCCATT
TTGGTACCCCAGGCTATGGGAGCCCTCACTTCACTGCACTGTGCTCCTCAGTCCCTTTCCCTGAGGGGGAAGCCTTTCCC
CCTGTCTCTGTCACCACTCTGGGCTCTCCATGCATTCAAAC

ORF - retro_pabe_3294 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.25 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMAGHLASDFAFSPPPGGGGDGPGG-PEPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEV-WG-IPPCPPPY
MAGHL.SDFAFSPPPGG.GDGPGG.P..GWVDPRTWLSFQGPPGGPGIGPGVGPG.E..WG.IPPCPPPY
RetrocopyMAGHLTSDFAFSPPPGGAGDGPGG<PKTGWVDPRTWLSFQGPPGGPGIGPGVGPGAEEPWG<IPPCPPPY
ParentalEFCGGMAYCGPQVGVGLVPQGSLETSQPEGEAGVGVESNSDGASPEPCTVPPGAVKLEKEKLEQNPEESQ
EFCGGMAYCGPQVGVGLVPQG.LETSQPEGEAGV.VESNSDGASPEPCT.PPGAVKLEKEKLEQNPEESQ
RetrocopyEFCGGMAYCGPQVGVGLVPQGCLETSQPEGEAGVRVESNSDGASPEPCTFPPGAVKLEKEKLEQNPEESQ
ParentalDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKW
DIKALQKELEQFAKLLKQKRITLGYTQADVGL.LGVLFGKVFSQTTICRFEALQLSFKN.C.LRPLLQKW
RetrocopyDIKALQKELEQFAKLLKQKRITLGYTQADVGLILGVLFGKVFSQTTICRFEALQLSFKNVCELRPLLQKW
ParentalVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVW
VEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLE.DVVRVW
RetrocopyVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLENDVVRVW
ParentalFCNRRQKGKRSSSDYAQREDFEAAGSPFSGG-PVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFP
FCNRRQ.GKRSSSDYAQRE.FEAAGSPFSGG.PVSFPLAPGPHFGTPGYGSPHFTAL.SSVPFPEGEAFP
RetrocopyFCNRRQNGKRSSSDYAQREHFEAAGSPFSGG>PVSFPLAPGPHFGTPGYGSPHFTALCSSVPFPEGEAFP
ParentalPVSVTTLGSP-MHSN
PVSVTTLGSP.MHSN
RetrocopyPVSVTTLGSP<MHSN

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 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .12 RPM
SRP007412_heart 0 .00 RPM 0 .12 RPM
SRP007412_kidney 0 .07 RPM 0 .36 RPM
SRP007412_liver 0 .00 RPM 0 .12 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3294 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3294 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3294 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2721

Parental genes homology:
Parental genes homology involve 25 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000103773 retrocopies
Bos taurus ENSBTAG000000211112 retrocopies
Canis familiaris ENSCAFG000000004851 retrocopy
Callithrix jacchus ENSCJAG000000197891 retrocopy
Dipodomys ordii ENSDORG000000095491 retrocopy
Equus caballus ENSECAG000000089671 retrocopy
Erinaceus europaeus ENSEEUG000000153572 retrocopies
Felis catus ENSFCAG000000010783 retrocopies
Gorilla gorilla ENSGGOG000000276623 retrocopies
Macropus eugenii ENSMEUG000000132213 retrocopies
Microcebus murinus ENSMICG000000015111 retrocopy
Myotis lucifugus ENSMLUG000000110283 retrocopies
Mustela putorius furoENSMPUG000000012022 retrocopies
Mus musculus ENSMUSG000000244062 retrocopies
Oryctolagus cuniculus ENSOCUG000000171603 retrocopies
Otolemur garnettii ENSOGAG000000006213 retrocopies
Ochotona princeps ENSOPRG000000039262 retrocopies
Pongo abelii ENSPPYG00000017210 3 retrocopies
retro_pabe_2761, retro_pabe_3294 , retro_pabe_898,
Pan troglodytes ENSPTRG000000179535 retrocopies
Pteropus vampyrus ENSPVAG000000073342 retrocopies
Rattus norvegicus ENSRNOG000000464874 retrocopies
Sus scrofa ENSSSCG000000013932 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000261033 retrocopies
Tupaia belangeri ENSTBEG000000130444 retrocopies
Tarsius syrichta ENSTSYG000000073404 retrocopies



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