RetrogeneDB ID:

retro_pabe_92

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2a:40700249..40701317(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000012328
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000004581
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_92
ATGGATGCCGGTGTGACTGAAAGTGGACTAAATGTGACTCTCACCATTCGGCTTCTTATGCACGGAAAGGAAGTAGGAAG
CATCATTGGGAAGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATT
GTCCTGAGAGAATCATCACTCTGACCGGCCCCACCAATGCCATCTTTAAGGCTTTCGCTATGATCATCGACAAGCTGGAG
GAAGATATCAACAGCTCCATGACCAACAGCACCGCGGCCAGCAGGCCCCCGGTCACCCTGAGGCTGGTGGTGCCGGCCAC
CCAGTGCGGCTCCCTGATTGGGAAAGGCGGGTGTAAGATCAAAGAGATCCGCGAGAGTACGGGGGCGCAGGTCCAGGTGG
CGGGGGATATGCTGCCCAACTCCACCGAGCGGGCCATCACCATCGCTGGCGTGCCGCAGTCTGTCACCGAGTGTGTCAAG
CAGATCTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGAAGAGTCATGACCATTCCGTACCAGCCCATGCC
GGCCAGCTCCCCAGTCATCTGCGCGGGCGGCCAAGATCGGTGCAGCGACGCTGCGGGCTACCCCCATGCCACCCATGACC
TGGAGGGACCACCTCTAGATGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTCGATCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACCGGATTCGCCGGAATTGACTCCAGCTCTCCAGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCATCTACTCAAACCACCCATGAACTCACCATTCCAAATAACTTAATTGGCTGCA
TAATCGGGCGCCAAGGCGCCAACATTAATGAGATCCGCCAGATGTCCGGGGCCCAGATCAAAATTGCCAACCCAGTGGAA
GGCTCCTCTGGTAGGCAGGTTACTATCACTGGCTCTGCTGCCAGTATTAGTCTGGCCCAGTATCTAATCAATGCCAGGCT
TTCCTCTGAGAAGGGCATGGGGTGCAGC

ORF - retro_pabe_92 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.58 %
Parental protein coverage: 57.73 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
RetrocopyMDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK
ParentalAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
RetrocopyAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
ParentalSTERAITIAGIPQSIIECVKQICVVMLES---PPKG--VTIPYRPKPSSSPVIFAGGQDRYSTGSDSASF
STERAITIAG.PQS..ECVKQIC.VMLE.....P.G...TIPY.P.P.SSPVI.AGGQDR.S...D.A..
RetrocopySTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCS---DAAGY
ParentalPHTT
PH.T
RetrocopyPHAT

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 119 .43 RPM 142 .87 RPM
SRP007412_cerebellum 68 .95 RPM 187 .51 RPM
SRP007412_heart 56 .08 RPM 89 .08 RPM
SRP007412_kidney 157 .08 RPM 230 .47 RPM
SRP007412_liver 146 .70 RPM 136 .24 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_92 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_92 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_92 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_175
Sus scrofa retro_sscr_61
Equus caballus retro_ecab_67
Oryctolagus cuniculus retro_ocun_10

Parental genes homology:
Parental genes homology involve 24 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000207571 retrocopy
Canis familiaris ENSCAFG000000068211 retrocopy
Callithrix jacchus ENSCJAG000000185902 retrocopies
Cavia porcellus ENSCPOG000000009672 retrocopies
Dasypus novemcinctus ENSDNOG000000086886 retrocopies
Equus caballus ENSECAG000000223891 retrocopy
Echinops telfairi ENSETEG000000147413 retrocopies
Homo sapiens ENSG000001971112 retrocopies
Gorilla gorilla ENSGGOG000000126132 retrocopies
Macropus eugenii ENSMEUG000000018877 retrocopies
Microcebus murinus ENSMICG000000116512 retrocopies
Myotis lucifugus ENSMLUG000000099713 retrocopies
Macaca mulatta ENSMMUG000000066082 retrocopies
Mus musculus ENSMUSG000000568511 retrocopy
Nomascus leucogenys ENSNLEG000000176931 retrocopy
Oryctolagus cuniculus ENSOCUG000000224903 retrocopies
Pongo abelii ENSPPYG00000004581 2 retrocopies
retro_pabe_3346, retro_pabe_92 ,
Pongo abelii ENSPPYG000000193273 retrocopies
Pan troglodytes ENSPTRG000000050181 retrocopy
Pteropus vampyrus ENSPVAG000000122843 retrocopies
Rattus norvegicus ENSRNOG000000368522 retrocopies
Sus scrofa ENSSSCG000000002741 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000036352 retrocopies
Vicugna pacos ENSVPAG000000004061 retrocopy



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