RetrogeneDB ID:

retro_pabe_568

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:10:8467406..8468220(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP0
Ensembl ID:ENSPPYG00000005022
Aliases:None
Description:ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]


Retrocopy-Parental alignment summary:






>retro_pabe_568
ATGCCCAGGGAAGACAGGGCGACATGGAAATCCAACTACTTCCTTAAGATCATCCAACTATTGGATGATTATCCGAAATG
TTTCATCGTGGGAGCAGACAATGTGGGCTCCAAGCAGATGCAGCAGATCCTCATGTCCCTTCATGGGAAGGCCGTGGTGC
TGATGGGCAAGAACACCATGATGCGCAAGGCCATCCGAGGGCACCTGGAAAACAACCCAACTCTGGAGAAACTGCTGCCT
CATATCCGGGGGAATGTGGGCTTTGTGTTCACCAAGGAGGACCTCACTGAGATCAGGGACATGTTGCTGGCCAATAAGGT
GCCAGCTGCTGCCCGTGCTGGTGCCATTGCCCCATGTGAAGTCACTGTGCCAGCCCAGAACACTGCTCGGGCCCGAGAAG
ACCTCCTTTTTCCAGGCTTTAGGTATCACCACTAAAATCCCCAGAGGCACCATTGAAATCCTGAGTGATGTGCAGCTGAT
CAAGACTGGAAACAAAGTGGGAGCCAGCGAAGCCACGCTGCTGAACATGCTCAACATCTCCCCCTTCTCCTTTGGGCTGG
TCATCCAGCAGGTGTTCGACAATGGCAGCATCTACAGCCCTGAAGTGCTTGACATCACAGAGGAAACTCTGCATTCTCGC
TTCCTGGAGGGTGTCCGCAATGTTGCCAGTGTCTGTCTGCAGATTGGCTACCCAACTGTTGCATCAGTACCCCATTCTAT
CATCAACGGGTACAAACGAGTCCTGGCCTTGTCTGTGGAGACGGATTACACCTTCCCACTTGCTGAAAAGGTCAAGGCCT
TCTTGGCTGATCCA

ORF - retro_pabe_568 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.35 %
Parental protein coverage: 85.8 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQI.MSL.GKAVVLMGKNTMMRKAIRGHLE
RetrocopyMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQILMSLHGKAVVLMGKNTMMRKAIRGHLE
ParentalNNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTG-LGP-EKTSFF
NNP.LEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNT...GP.EKTSFF
RetrocopyNNPTLEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTA<SGP<EKTSFF
ParentalQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITE
QALGITTKI.RGTIEILSDVQLIKTG.KVGASEATLLNMLNISPFSFGLVIQQVFDNGSIY.PEVLDITE
RetrocopyQALGITTKIPRGTIEILSDVQLIKTGNKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYSPEVLDITE
ParentalETLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADP
ETLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADP
RetrocopyETLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADP

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 .17 RPM 45 .12 RPM
SRP007412_cerebellum 0 .12 RPM 35 .14 RPM
SRP007412_heart 0 .27 RPM 90 .94 RPM
SRP007412_kidney 0 .30 RPM 179 .03 RPM
SRP007412_liver 0 .28 RPM 180 .30 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_568 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_568 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_568 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 30 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000037562 retrocopies
Ailuropoda melanoleuca ENSAMEG000000051444 retrocopies
Canis familiaris ENSCAFG000000102275 retrocopies
Choloepus hoffmanni ENSCHOG000000027452 retrocopies
Callithrix jacchus ENSCJAG000000086773 retrocopies
Cavia porcellus ENSCPOG000000218125 retrocopies
Equus caballus ENSECAG000000158162 retrocopies
Erinaceus europaeus ENSEEUG000000075531 retrocopy
Felis catus ENSFCAG000000133541 retrocopy
Homo sapiens ENSG000000891577 retrocopies
Gorilla gorilla ENSGGOG000000265825 retrocopies
Macropus eugenii ENSMEUG0000001640912 retrocopies
Myotis lucifugus ENSMLUG0000000197011 retrocopies
Macaca mulatta ENSMMUG000000091572 retrocopies
Mustela putorius furoENSMPUG000000030554 retrocopies
Mus musculus ENSMUSG000000672742 retrocopies
Nomascus leucogenys ENSNLEG0000000029211 retrocopies
Oryctolagus cuniculus ENSOCUG000000057492 retrocopies
Otolemur garnettii ENSOGAG000000038434 retrocopies
Procavia capensis ENSPCAG000000164296 retrocopies
Petromyzon marinus ENSPMAG000000013391 retrocopy
Pongo abelii ENSPPYG00000005022 5 retrocopies
Pteropus vampyrus ENSPVAG000000031103 retrocopies
Rattus norvegicus ENSRNOG000000011483 retrocopies
Sarcophilus harrisii ENSSHAG000000016232 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000113274 retrocopies
Tupaia belangeri ENSTBEG000000054981 retrocopy
Tarsius syrichta ENSTSYG000000097327 retrocopies
Tursiops truncatus ENSTTRG000000056581 retrocopy
Vicugna pacos ENSVPAG000000121562 retrocopies



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