RetrogeneDB ID:

retro_pabe_2346

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:131682008..131682955(-)
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:ENSPPYG00000017976
Aliases:None
Description:IMP (inosine 5'-monophosphate) dehydrogenase 1 [Source:HGNC Symbol;Acc:6052]


Retrocopy-Parental alignment summary:






>retro_pabe_2346
CGCAGCAGCATGGCGGACTACCTGATCAGCGGCAGCACCAGCTACGTGCGCAAGGATGGGCTCACTGCGCCCCAGCTCTT
CGCCAGCGCTGACGGCCTCACTCACAACAACTTCCTGATTCTCCTAGGATTCATAGACTTCATAGCTGATGAGGTGGACC
TGACCTCAGCCCTGAACCGGAAGGTCACGCTGAAGACGCCGCTGATCTCCTCCCCTATGGACACTGTGACAGAGGCTGAC
ATGGCCATCGCGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTGCACCGCAGAGTTCCAGGCCAACGAGGT
GCGGAAGATCAAGAAGTTTGAACAGGGCTTCATCACGGACCCCGTGGTGCTGAGCCCCTCGGACACTGTGGGTGATGTGC
TGGAGGCCAAGATGCGGCATGGCTTCTCTGGCATCCGCATCACTAGACGGGCACCATAGGCAGCAAGCTATTGGGCATTG
TCACCTCCCAAGACACTGACTTTCTTGCTGAGAAGGACACCACCACCCTCCTCAGCGAGGTGATGACGCCAAGGATTGAG
CTGGTGGTGGCTCCAGCAGGTGTGACGTTGAAAGAGGCAAAAGAGATCCTAAGTGTAGCGAGAAAGGGAAGCTGCCTATC
GTCAATGATCGCGATGAACTGGTGGCCATCATCACCCACACCGACCTGAAGAAGAACTGAGACTACCCTCTGGCCTCCAA
GGATTCCCACAAGCAGCTGCTGTGCAGGGCAGCTGTGGGCACCCGTGAGGATGAAAAATACTGCCTGGACCTGCTCTCCC
AGGCGGGCGTCAACATATAGTCTTGGACTCGTCCCAGGGAACTCGGCATATCAGATCACCATGGTGCATTACATCAAACA
AAAGTACCCCCACCTCCAGGTGATTGGGGGGAACATGGTGACAGCAGCCCAGGCCAAGAACCTGATG

ORF - retro_pabe_2346 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.67 %
Parental protein coverage: 53.55 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalRASMADYLISGGTGYVPEDGLTEQKNFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLIS
R.SMADYLISG.T.YV..DGLT....FASADGLT.N.FLIL.GFIDFIADEVDLTSAL.RK.TLKTPLIS
RetrocopyRSSMADYLISGSTSYVRKDGLTAPQLFASADGLTHNNFLILLGFIDFIADEVDLTSALNRKVTLKTPLIS
ParentalSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRH
SPMDTVTEADMAIAMALMGGIGFIHHNCT.EFQANEVRK.KKFEQGFITDPVVLSPS.TVGDVLEAKMRH
RetrocopySPMDTVTEADMAIAMALMGGIGFIHHNCTAEFQANEVRKIKKFEQGFITDPVVLSPSDTVGDVLEAKMRH
ParentalGFSGIPITE-TGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEIL-QRSK
GFSGI.IT..TGT.GSKL.GIVTS.D.DFLAEKD.TTLLSEVMTPRIELVVAPAGVTLKEA.EIL...S.
RetrocopyGFSGIRITR<TGTIGSKLLGIVTSQDTDFLAEKDTTTLLSEVMTPRIELVVAPAGVTLKEAKEIL<KCSE
ParentalKGKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDV-IVLD
KGKLPIVNDRDELVAII..TDLKKN.DYPLASKDS.KQLLC.AAVGTRED.KY.LDLL.QAGV...IVLD
RetrocopyKGKLPIVNDRDELVAIITHTDLKKN*DYPLASKDSHKQLLCRAAVGTREDEKYCLDLLSQAGVNI<IVLD
ParentalSSQ-GNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLI
SSQ.GNS.YQI.MVHYIKQKYPHLQVIGGN.VTAAQAKNL.
RetrocopySSQ<GNSAYQITMVHYIKQKYPHLQVIGGNMVTAAQAKNLM

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 .83 RPM 16 .92 RPM
SRP007412_cerebellum 1 .09 RPM 9 .12 RPM
SRP007412_heart 0 .12 RPM 3 .31 RPM
SRP007412_kidney 0 .13 RPM 8 .88 RPM
SRP007412_liver 0 .09 RPM 5 .17 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2346 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2346 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2346 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 ENSPPYG000000138841 retrocopy
Pongo abelii ENSPPYG00000017976 7 retrocopies
Pan troglodytes ENSPTRG000000196607 retrocopies



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