RetrogeneDB ID:

retro_pabe_3732

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:27644331..27644842(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTP4A1
Ensembl ID:ENSPPYG00000016743
Aliases:PTP4A1, PRL1
Description:protein tyrosine phosphatase type IVA 1 [Source:RefSeq peptide;Acc:NP_001126324]


Retrocopy-Parental alignment summary:






>retro_pabe_3732
ATGGCTAGAACGAACCTCCCTGCTTCTGTGGACACTGCATACAAAAATGTGAGATTTCTTATTACACACCACCCAACCAA
TACCTACTTTAATAGATTCTTACAGGAACTTAAGCAGAATGGAGTTACCACCATAGTAAGAGTATGAAAAGCAACTTACA
ACATTGCTCTTTTGGAGAAGGAAAGCATCCAGGTTCCGGACTGGCCTTTTGATGATGGTACAGCACCATCCAGCCAGATA
ATTGATAACTGGTTAAAACTTATGAAAAATAAATTTCGTGAAGATCCTGGTTGTTGTATTGCAATTCACTGTGTTGTAGG
TTTTGGGTGAGCTCCAGTTGCTAGTTGCCGTAGCTTTAATTGAAGGTGGAATGAAATATGAAGATGTAGTACAGTTCATC
AGATAAAAGTGACATGGAGCTTTTAACAGCAAACAACTTTTGTATTTGGAGAAATATTGTCTTAAAATATGCTTGCACCT
CAGAAATCCCAGAAATAACTGTTTCCTTCAG

ORF - retro_pabe_3732 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.24 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTALVEKEGIHVLDWPF
MAR.N.PA.V...YKN.RFLITH.PTN...N.F..ELK..GVTTIVRV..ATY..AL.EKE.I.V.DWPF
RetrocopyMARTNLPASVDTAYKNVRFLITHHPTNTYFNRFLQELKQNGVTTIVRV*KATYNIALLEKESIQVPDWPF
ParentalDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPV-LVALALIEGGMKYEDAVQFIRQKRRG
DDG..PS.QI.D.WL.L.K.KFRE.PGCCIA.HCV.G.G.APV.LVA.ALIEGGMKYED.VQFIR.K..G
RetrocopyDDGTAPSSQIIDNWLKLMKNKFREDPGCCIAIHCVVGFG*APV>LVAVALIEGGMKYEDVVQFIR*K*HG
ParentalAFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCIQ
AFNSKQLLYLEKY..K..L........RNNC..Q
RetrocopyAFNSKQLLYLEKYCLKICLHLRNP---RNNCFLQ

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 29 .36 RPM
SRP007412_cerebellum 0 .00 RPM 24 .56 RPM
SRP007412_heart 0 .00 RPM 30 .52 RPM
SRP007412_kidney 0 .00 RPM 31 .12 RPM
SRP007412_liver 0 .00 RPM 310 .82 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3732 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3732 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3732 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4798
Pan troglodytes retro_ptro_3190
Gorilla gorilla retro_ggor_2986
Sus scrofa retro_sscr_1186
Equus caballus retro_ecab_10

Parental genes homology:
Parental genes homology involve 31 parental genes, and 138 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024383 retrocopies
Bos taurus ENSBTAG000000022753 retrocopies
Canis familiaris ENSCAFG000000024903 retrocopies
Callithrix jacchus ENSCJAG000000017433 retrocopies
Cavia porcellus ENSCPOG000000257595 retrocopies
Dasypus novemcinctus ENSDNOG000000185074 retrocopies
Dipodomys ordii ENSDORG000000099606 retrocopies
Equus caballus ENSECAG000000224836 retrocopies
Erinaceus europaeus ENSEEUG000000064773 retrocopies
Echinops telfairi ENSETEG000000081836 retrocopies
Felis catus ENSFCAG000000011993 retrocopies
Homo sapiens ENSG000001122455 retrocopies
Gorilla gorilla ENSGGOG000000225217 retrocopies
Latimeria chalumnae ENSLACG000000071831 retrocopy
Loxodonta africana ENSLAFG000000065728 retrocopies
Myotis lucifugus ENSMLUG000000011621 retrocopy
Macaca mulatta ENSMMUG000000027771 retrocopy
Monodelphis domestica ENSMODG000000187015 retrocopies
Mustela putorius furoENSMPUG000000031181 retrocopy
Mus musculus ENSMUSG0000002606410 retrocopies
Nomascus leucogenys ENSNLEG000000004406 retrocopies
Oryctolagus cuniculus ENSOCUG000000063114 retrocopies
Pongo abelii ENSPPYG000000016063 retrocopies
Pongo abelii ENSPPYG00000016743 5 retrocopies
Pan troglodytes ENSPTRG000000183144 retrocopies
Pteropus vampyrus ENSPVAG000000152252 retrocopies
Rattus norvegicus ENSRNOG000000117714 retrocopies
Rattus norvegicus ENSRNOG000000463704 retrocopies
Tupaia belangeri ENSTBEG0000000995614 retrocopies
Tarsius syrichta ENSTSYG000000046322 retrocopies
Tursiops truncatus ENSTTRG000000041296 retrocopies



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