RetrogeneDB ID:

retro_ptro_1631

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2A:112061078..112061810(-)
Located in intron of:ENSPTRG00000012358
Retrocopy
information
Ensembl ID:ENSPTRG00000039415
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C14ORF166
Ensembl ID:ENSPTRG00000006344
Aliases:None
Description:Pan troglodytes UPF0568 protein C14orf166-like (C14H14orf166), mRNA. [Source:RefSeq mRNA;Acc:NM_001246406]


Retrocopy-Parental alignment summary:






>retro_ptro_1631
ATGTTCCAATGCAAGCTGACGGCTCTCGACTACCACAACCCTGCCGGTTTCAACTGCAAAGATGAAACAGAATTTAGAAA
CTTCACTGTTTGGCTTGAAGACCAGAAAATCAGACACTACAAGATTGAAGACAGAGGTAATTTAAGAAACATCCACAGCA
GCGACTGGCCTGAGTTCTTTCAAAAGTATCTCAGAGATGTTAACTGTTGTTTAAAGATTCAAGATCGACAAGAAGCTATT
GACTGGCTTCTTGGTTTAGCTGTTAGATTTGAATATGGAGATAATGCTGAAAAATACAAGGACTTAGTACCTGATAATGC
AAAAACTGCTGACAATGCAACTAAAAATGCAGAACGATTGATAAATTTGGACGTAAATAATCCTGATTTTAAGCCTGGTG
TAATGGCTTTGGCTAACCTGCTTCAGGTTCAATGTCATGATGATTGCCTGGTAATGCTTAAGGCAATTCAAATTTTGGTT
CAGGAGCACCTGACACAGGATGCAGTTGCTAAAGCAAATCAAACAAAAGAGGGCTTGCCTGTTGCTTTAGACAAACATAT
TCTTGGTTTTGACACAGGAGATGCAGTTCTTAATGAAGCTACTCAAATTCTGTGATTGCTGCATACAGAAGAGCTCAGAC
AGCTACAGACAAAAATTAATGAAGCCATAGCAGCTGTTCAGGCAATTATTGCTGATGCAAGGACAGACCACAGGCTGGGA
AAAGTTGGAAGA

ORF - retro_ptro_1631 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.57 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFRRKLTALDYHNPAGFNCKDETEFRNFIVWLEDQKIRHYKIEDRGNLRNIHSSDWPKFFEKYLRDVNCP
MF..KLTALDYHNPAGFNCKDETEFRNF.VWLEDQKIRHYKIEDRGNLRNIHSSDWP.FF.KYLRDVNC.
RetrocopyMFQCKLTALDYHNPAGFNCKDETEFRNFTVWLEDQKIRHYKIEDRGNLRNIHSSDWPEFFQKYLRDVNCC
ParentalFKIQDRQEAIDWLLGLAVRLEYGDNAEKYKDLVPDNSKTADNATKNAEPLINLDVNNPDFKAGVMALANL
.KIQDRQEAIDWLLGLAVR.EYGDNAEKYKDLVPDN.KTADNATKNAE.LINLDVNNPDFK.GVMALANL
RetrocopyLKIQDRQEAIDWLLGLAVRFEYGDNAEKYKDLVPDNAKTADNATKNAERLINLDVNNPDFKPGVMALANL
ParentalLQIQRHDDYLVMLKAIRILVQERLTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEAAQILRLLHIE
LQ.Q.HDD.LVMLKAI.ILVQE.LTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEA.QIL.LLH.E
RetrocopyLQVQCHDDCLVMLKAIQILVQEHLTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEATQIL*LLHTE
ParentalELRELQTKINEAIVAVQAIIADPKTDHRLGKVGR
ELR.LQTKINEAI.AVQAIIAD..TDHRLGKVGR
RetrocopyELRQLQTKINEAIAAVQAIIADARTDHRLGKVGR

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 24 .88 RPM
SRP007412_cerebellum 0 .04 RPM 28 .68 RPM
SRP007412_heart 0 .03 RPM 64 .03 RPM
SRP007412_kidney 0 .10 RPM 56 .91 RPM
SRP007412_liver 0 .00 RPM 40 .49 RPM
SRP007412_testis 0 .21 RPM 79 .14 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1631 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1631 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1631 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2307
Pongo abelii retro_pabe_1980

Parental genes homology:
Parental genes homology involve 29 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000020832 retrocopies
Canis familiaris ENSCAFG000000146484 retrocopies
Callithrix jacchus ENSCJAG000000069263 retrocopies
Cavia porcellus ENSCPOG000000013176 retrocopies
Dasypus novemcinctus ENSDNOG000000032483 retrocopies
Dipodomys ordii ENSDORG000000123351 retrocopy
Equus caballus ENSECAG000000126001 retrocopy
Erinaceus europaeus ENSEEUG000000155831 retrocopy
Felis catus ENSFCAG000000026633 retrocopies
Homo sapiens ENSG000000873021 retrocopy
Loxodonta africana ENSLAFG000000031621 retrocopy
Microcebus murinus ENSMICG000000087201 retrocopy
Myotis lucifugus ENSMLUG000000086436 retrocopies
Macaca mulatta ENSMMUG000000182002 retrocopies
Monodelphis domestica ENSMODG000000132111 retrocopy
Mustela putorius furoENSMPUG000000052536 retrocopies
Mus musculus ENSMUSG000000218072 retrocopies
Nomascus leucogenys ENSNLEG000000124061 retrocopy
Oryctolagus cuniculus ENSOCUG000000146811 retrocopy
Otolemur garnettii ENSOGAG000000132325 retrocopies
Ochotona princeps ENSOPRG000000163522 retrocopies
Pongo abelii ENSPPYG000000058141 retrocopy
Pan troglodytes ENSPTRG00000006344 1 retrocopy
retro_ptro_1631 ,
Pteropus vampyrus ENSPVAG000000133921 retrocopy
Sus scrofa ENSSSCG000000050291 retrocopy
Tupaia belangeri ENSTBEG000000138985 retrocopies
Tarsius syrichta ENSTSYG000000045286 retrocopies
Tursiops truncatus ENSTTRG000000057211 retrocopy
Vicugna pacos ENSVPAG000000114431 retrocopy



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