RetrogeneDB ID:

retro_ptro_1670

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2B:206942256..206942863(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA2
Ensembl ID:ENSPTRG00000019120
Aliases:None
Description:Proteasome subunit alpha type [Source:UniProtKB/TrEMBL;Acc:H2R5C6]


Retrocopy-Parental alignment summary:






>retro_ptro_1670
ATGGCGGAGCGCGGTACGGCTTTTCGCTGACTACATTCAGCCCGTCTGATAAACTTGTCCGGATTGAATATGCTTTGGCT
GCTATAGCTGGAGGAGCCCTGTCAGTGGGAATTAAAGCGGCAAATGGTGTGGTATTAGCAACCGAGAAAAAACAGAAATT
CATTCTGTATGATGAGCGAAGTGTAGACAAAGTGGAACCAATTACCAAGCACATAGGTTTGGTGTACAGTGGCGTGGGCC
CAGATAACAGAGTGCTTGTGCACACAGCTCGAAACTAGCTCAACAATACTATCTTGTGTACCAAGTGCCCATTCCCACAG
CTCAGCTAGTACGGAGAGTAGCTTCTGTGATGCAAGAATATACCCAGTCAGGTGGTGTTTGTCCATTTGGAGTTTCTTTA
CTTGTTTGTGGTTGGAATGAGGGACAACCATATTTATTTCAGTCAGATCCATCTGGAGCTTACTTGGCCTGGAAAGCCAC
AGCAGTGGGAAAGAACTATGTGAATGGGAAAACTTCCCTTGAGAAAAGATAAAATGAAGATCTGGAACTTGAAGATGCCA
TTCATACAGCCATGTTAACCCTAAAGGAAAGCTTTGAAGGCCAAATG

ORF - retro_ptro_1670 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.27 %
Parental protein coverage: 86.75 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAERG-YSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPIT
MAERG.Y.FSLTTFSPS.KLV.IEYALAA.AGGA.SVGIKAANGVVLATEKKQK.ILYDERSV.KVEPIT
RetrocopyMAERG<YGFSLTTFSPSDKLVRIEYALAAIAGGALSVGIKAANGVVLATEKKQKFILYDERSVDKVEPIT
ParentalKHIGLVYSGMGPDYRVLVHRAR-KLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICG
KHIGLVYSG.GPD.RVLVH.AR.KLAQQYYLVYQ.PIPTAQLV.RVASVMQEYTQSGGV.PFGVSLL.CG
RetrocopyKHIGLVYSGVGPDNRVLVHTAR<KLAQQYYLVYQVPIPTAQLVRRVASVMQEYTQSGGVCPFGVSLLVCG
ParentalWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQM
WNEG.PYLFQSDPSGAY.AWKATA.GKNYVNGKT.LEKR.NEDLELEDAIHTA.LTLKESFEGQM
RetrocopyWNEGQPYLFQSDPSGAYLAWKATAVGKNYVNGKTSLEKR*NEDLELEDAIHTAMLTLKESFEGQM

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 .02 RPM 27 .15 RPM
SRP007412_cerebellum 0 .07 RPM 33 .20 RPM
SRP007412_heart 0 .00 RPM 49 .34 RPM
SRP007412_kidney 0 .00 RPM 64 .31 RPM
SRP007412_liver 0 .00 RPM 79 .09 RPM
SRP007412_testis 1 .48 RPM 57 .64 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1670 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1670 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1670 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2199
Pongo abelii retro_pabe_2076
Macaca mulatta retro_mmul_923

Parental genes homology:
Parental genes homology involve 24 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000094333 retrocopies
Bos taurus ENSBTAG000000009903 retrocopies
Choloepus hoffmanni ENSCHOG000000006441 retrocopy
Callithrix jacchus ENSCJAG000000077304 retrocopies
Cavia porcellus ENSCPOG000000131341 retrocopy
Dasypus novemcinctus ENSDNOG000000119102 retrocopies
Echinops telfairi ENSETEG000000158352 retrocopies
Homo sapiens ENSG000001065882 retrocopies
Gorilla gorilla ENSGGOG000000065381 retrocopy
Myotis lucifugus ENSMLUG000000100862 retrocopies
Macaca mulatta ENSMMUG000000224512 retrocopies
Mustela putorius furoENSMPUG000000181451 retrocopy
Mus musculus ENSMUSG000000156714 retrocopies
Nomascus leucogenys ENSNLEG000000031771 retrocopy
Oryctolagus cuniculus ENSOCUG000000120921 retrocopy
Otolemur garnettii ENSOGAG000000168051 retrocopy
Ochotona princeps ENSOPRG000000117932 retrocopies
Pongo abelii ENSPPYG000000176122 retrocopies
Pan troglodytes ENSPTRG00000019120 2 retrocopies
retro_ptro_1670 , retro_ptro_628,
Rattus norvegicus ENSRNOG000000499202 retrocopies
Sus scrofa ENSSSCG000000207693 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000133341 retrocopy
Tarsius syrichta ENSTSYG000000142992 retrocopies
Tursiops truncatus ENSTTRG000000056491 retrocopy



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