RetrogeneDB ID:

retro_pabe_3485

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:67391457..67391811(-)
Located in intron of:ENSPPYG00000019291
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS20
Ensembl ID:ENSPPYG00000018600
Aliases:None
Description:ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]


Retrocopy-Parental alignment summary:






>retro_pabe_3485
ATGGCTTTTAAGGATACTGGAAAAACACCCATGGAGCCGAAGATGGCAATTCACCGAATTCGAATCACTCTAACAAGCTG
CAACGTAAAATCCCTGGGGAAGGTGTGTGCTGACTTGATCAGAGGAGCAAAGGAAAAGAATCTCAAAGTGAAAAGACCAG
TTCAAATGCCTACTAAGACTTTGAGAATCACACAAGAAAAAACTCCATGTGGTGAAGGTTCTAAGCCATGGGATCATTTC
CAGATGAGAATCCACAAGCGACTCATTGACTTGCACAGTCCTTCTGAGATTGTTAAGCAGATTACTTCCATAAGTATTGA
GCCAGGAGTTGAGATGGAAGTCACCATTGTAGAC

ORF - retro_pabe_3485 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.98 %
Parental protein coverage: 99.16 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPC
MAFKDTGKTP.EP..AIHRIRITLTS.NVKSL.KVCADLIRGAKEKNLKVK.PV.MPTKTLRIT..KTPC
RetrocopyMAFKDTGKTPMEPKMAIHRIRITLTSCNVKSLGKVCADLIRGAKEKNLKVKRPVQMPTKTLRITQEKTPC
ParentalGEGSKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIAD
GEGSK.WD.FQMRIHKRLIDLHSPSEIVKQITSISIEPGVE.EVTI.D
RetrocopyGEGSKPWDHFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEMEVTIVD

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 91 .06 RPM
SRP007412_cerebellum 0 .00 RPM 60 .68 RPM
SRP007412_heart 0 .00 RPM 97 .78 RPM
SRP007412_kidney 0 .03 RPM 173 .72 RPM
SRP007412_liver 0 .00 RPM 152 .92 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3485 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3485 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3485 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4271
Pan troglodytes retro_ptro_2897
Gorilla gorilla retro_ggor_2857

Parental genes homology:
Parental genes homology involve 22 parental genes, and 304 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000001914711 retrocopies
Canis familiaris ENSCAFG0000002988420 retrocopies
Callithrix jacchus ENSCJAG000000166314 retrocopies
Dipodomys ordii ENSDORG000000057942 retrocopies
Echinops telfairi ENSETEG000000033943 retrocopies
Felis catus ENSFCAG0000002923322 retrocopies
Homo sapiens ENSG0000000898826 retrocopies
Gorilla gorilla ENSGGOG0000000183721 retrocopies
Macropus eugenii ENSMEUG0000001417121 retrocopies
Monodelphis domestica ENSMODG000000091146 retrocopies
Mustela putorius furoENSMPUG0000001045215 retrocopies
Mus musculus ENSMUSG000000282347 retrocopies
Nomascus leucogenys ENSNLEG0000000121419 retrocopies
Oryctolagus cuniculus ENSOCUG0000000306817 retrocopies
Otolemur garnettii ENSOGAG0000000776010 retrocopies
Ochotona princeps ENSOPRG0000001104211 retrocopies
Procavia capensis ENSPCAG000000043003 retrocopies
Pongo abelii ENSPPYG00000018600 30 retrocopies
Pan troglodytes ENSPTRG0000002026427 retrocopies
Rattus norvegicus ENSRNOG000000085557 retrocopies
Sarcophilus harrisii ENSSHAG0000001120010 retrocopies
Sus scrofa ENSSSCG0000000624912 retrocopies



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