RetrogeneDB ID:

retro_ptro_2172

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:98483546..98484263(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000038674
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSME2
Ensembl ID:ENSPTRG00000006196
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2172
ATGGCCAAGCCGTGTGGGGCGCGCCTGAGCGGAGAAGCCCTTAAACAGGTGGAGGTCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAAGAATTCCTCTGCAGATTCTTGCTACAGAAAATCATATATGTGAATCAGCTCTTGCAAGAGGACTCCCTCAATG
TGGCTGACCTGACTTCCCTCCGGGCCCCACTGGACGTCCCCATCCCAGACCCTCCACCCAAGGATGATGAGATGGAAACA
GATAAGCAGGAGAAGAAAGAAGTCCCTAAGTGTGGACTTCTCCCTGGGGATGAGAAAGTCCTGTCCCTCTTTGCCCTGGT
TAAGCCAGAAGTCTGGACTCTCAAAGAGAAATGCATTCTGCTGATTACGTGGATCCAACACCTGATCCCCAAGATTGACG
ATGGAAATGAGTTTGGGGTAGCAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCCGTCAAGACCAAAGTGGAAGCTTTC
CAGACAACCATTTCCAAGTACTTCTCAGAACGTGGGGATGCTGTGGCCAAGGCCTCCAAGGAGACTCATGTAATGGATTA
CTGGGCCTTGGTGCATGAACGAGATGAGGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACCTGAGGGCCTTCTATG
CTGAGCTTTATCATATCATCAGCAGCAACTTGTAGAAAATTGTCAACCCAAAGGTTGAAGAGAAGCCATCTATGTAC

ORF - retro_ptro_2172 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.72 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVADLTSLRAPLDIPIPD
MAKPCG.RLSGEA.KQVEVFRQNLFQEAEEFL.RFL.QKIIY.NQLLQEDSLNVADLTSLRAPLD.PIPD
RetrocopyMAKPCGARLSGEALKQVEVFRQNLFQEAEEFLCRFLLQKIIYVNQLLQEDSLNVADLTSLRAPLDVPIPD
ParentalPPPKDDEMETDKQEKKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGV
PPPKDDEMETDKQEKKEVPKCG.LPG.EKVLSL.ALVKPEVWTLKEKCIL.ITWIQHLIPKI.DGN.FGV
RetrocopyPPPKDDEMETDKQEKKEVPKCGLLPGDEKVLSLFALVKPEVWTLKEKCILLITWIQHLIPKIDDGNEFGV
ParentalAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLDLR
AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDY.ALVHERDEAAYGELRAMVLDLR
RetrocopyAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYWALVHERDEAAYGELRAMVLDLR
ParentalAFYAELYHIISSNLEKIVNPKGEEKPSMY
AFYAELYHIISSNL.KIVNPK.EEKPSMY
RetrocopyAFYAELYHIISSNL*KIVNPKVEEKPSMY

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 .05 RPM 40 .79 RPM
SRP007412_cerebellum 0 .04 RPM 45 .28 RPM
SRP007412_heart 0 .06 RPM 39 .96 RPM
SRP007412_kidney 0 .16 RPM 104 .35 RPM
SRP007412_liver 0 .36 RPM 202 .36 RPM
SRP007412_testis 0 .00 RPM 19 .50 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2172 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2172 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2172 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3222
Gorilla gorilla retro_ggor_2188
Pongo abelii retro_pabe_2669

Parental genes homology:
Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000071673 retrocopies
Homo sapiens ENSG000001009114 retrocopies
Gorilla gorilla ENSGGOG000000160254 retrocopies
Macaca mulatta ENSMMUG000000124734 retrocopies
Mus musculus ENSMUSG000000791971 retrocopy
Nomascus leucogenys ENSNLEG000000152604 retrocopies
Otolemur garnettii ENSOGAG000000165841 retrocopy
Pongo abelii ENSPPYG000000056844 retrocopies
Pan troglodytes ENSPTRG00000006196 4 retrocopies
Pan troglodytes ENSPTRG000000092251 retrocopy



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