RetrogeneDB ID:

retro_ptro_1724

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2B:191593492..191594400(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IMPDH1
Ensembl ID:ENSPTRG00000019660
Aliases:None
Description:Inosine-5'-monophosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:H2QVB7]


Retrocopy-Parental alignment summary:






>retro_ptro_1724
TTGTCACCTCCAGAGACATCAACTTTCTTGCTGAGGAGGACCACACCACCCTCCTCAGTGTTGGCTCCAGCAGGCCTGAT
GTTGAAAGAGGCAAATGAGATCCTGCAGCATAGCAAGAAAGGGAAGCTGTCTTTCGTCAATGATCCGATGAGCTGGTGGC
CATGATCACCTGCACCGACCTGAAGAAGAACAGAGACTACCCTCTGGCCTCCAAGGATTCCCACAAGCAGCTACTGCGCG
GGGCAGCTGTGGGCACCCCTGAGGATGACAAATACCGCCTGGACTTGCTCACCCAGGCGGGGGTAGACGTCGTAGTCTTG
GACTCGTCCCAAGGGAACTCGGTGTATCAGATTGCCACGGTGCATTACATCAAACAGAAGTACCCCCACCTCCAGGTGAT
TGGGATGACAGCCGCCCAGGCCAAAAACCTGATTGACGCTGCGGTGGACGGGCTGCGCATAGGTATGGGCTGCGGCTCCA
TCTGCATCACCCAGGAAGTGATGGCCTGCGGTGGTCCCCAGGGCACTGCATTGTACAAGGTGGCCGAGTATGCCCTGTGC
TTTGGTGTGTCCATCATAGCCGATGGCGGCATCTAGACCGTGGGGCACGTGGTTAAGGCCCTGGCCCTTGGAGCCTCCAC
AGTGATGATGGGCTCCCTGCTGGCCACCACCACGTAGGACCCCGGCGAGTATTTCTTCTCAGATGGGGTGCAGCTCAAGA
AGTACCAGGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGCAGCAGCCAGAAATGATACGTCAGCAAGGGGAATAAG
GTGAAGATCGCGCAGGGTGTCTTGGGCTCCATCCAGGACAAAGGATCCATTCATAAGTTCGTGTCCTACCTCATAGCGGG
CATCCAGCCCGGCTGCCAGGATATCGGG

ORF - retro_ptro_1724 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.82 %
Parental protein coverage: 51.25 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGKLPIVND-RDELVAIIARTDLKKNRDYP
L......T.L....TP....V.APAG..LKEANEILQ.SKKGKL..VND..DELVA.I..TDLKKNRDYP
RetrocopyLSPPETSTFLLRRTTPPSS-VLAPAGLMLKEANEILQHSKKGKLSFVND<SDELVAMITCTDLKKNRDYP
ParentalLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYPHLQVIGGNV
LASKDS.KQLL.GAAVGT.EDDKYRLDLLTQAGVDV.VLDSSQGNSVYQIA.VHYIKQKYPHLQVIG...
RetrocopyLASKDSHKQLLRGAAVGTPEDDKYRLDLLTQAGVDVVVLDSSQGNSVYQIATVHYIKQKYPHLQVIG---
ParentalVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVV
.TAAQAKNLIDA.VDGLR.GMGCGSICITQEVMACG.PQGTA.YKVAEYA..FGV.IIADGGI.TVGHVV
RetrocopyMTAAQAKNLIDAAVDGLRIGMGCGSICITQEVMACGGPQGTALYKVAEYALCFGVSIIADGGI*TVGHVV
ParentalKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVS
KALALGASTVMMGSLLA.TT..PGEYFFSDGV.LKKY.GMGSLDAMEKSSSSQK.Y.S.G.KVKIAQGV.
RetrocopyKALALGASTVMMGSLLATTT*DPGEYFFSDGVQLKKYQGMGSLDAMEKSSSSQK*YVSKGNKVKIAQGVL
ParentalGSIQDKGSIQKFVPYLIAGIQHGCQDIG
GSIQDKGSI.KFV.YLIAGIQ.GCQDIG
RetrocopyGSIQDKGSIHKFVSYLIAGIQPGCQDIG

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 46 .92 RPM
SRP007412_cerebellum 0 .00 RPM 18 .03 RPM
SRP007412_heart 0 .00 RPM 6 .44 RPM
SRP007412_kidney 0 .00 RPM 12 .74 RPM
SRP007412_liver 0 .00 RPM 7 .14 RPM
SRP007412_testis 0 .32 RPM 4 .00 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1724 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1724 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1724 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 9 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000177701 retrocopy
Homo sapiens ENSG000001063487 retrocopies
Gorilla gorilla ENSGGOG000000039636 retrocopies
Macropus eugenii ENSMEUG000000160822 retrocopies
Macaca mulatta ENSMMUG000000145092 retrocopies
Nomascus leucogenys ENSNLEG000000123411 retrocopy
Pongo abelii ENSPPYG000000179767 retrocopies
Pan troglodytes ENSPTRG000000149081 retrocopy
Pan troglodytes ENSPTRG00000019660 7 retrocopies



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