RetrogeneDB ID:

retro_pabe_289

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:113162735..113163550(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PHB
Ensembl ID:ENSPPYG00000008920
Aliases:None
Description:prohibitin [Source:HGNC Symbol;Acc:8912]


Retrocopy-Parental alignment summary:






>retro_pabe_289
ATGACTGCCAAAGTGTTTGAGCTCATTAGCAAGTTTGGCCCACCCTTAGCTGTTGCAGGAGGTGTGGTGAACTCTGCCTT
ATATAATGTGGATGCTGGGTGCAGAGCCGCCATCTTTGACCAATTCCATGGAGTACAGAACATTGTGGCAGGGAAAGGAA
CTTACTTTTTTATCCCATGGATATAGAAACCAATTACCTTTGACTGCCATCTCAACCACGTAATGTGCCAGTCATCACAG
GTAGTAAAGATTTACAGAATGTCAACATCACACTCCACATCCTCTTCTGGTGTTTTGCTAGCCAGCTTCCTCATATCTAT
ACCAGCATTGGAAAGGACTATGATGAGCGTGTGCTGCTGTCCATCACTATAGAGATCCTCAGGTCAGTGGTGGCTCACTT
TGATGCTGGACAACTAATCACACAGAGAGAGCTGGTATCCAGGCAGGTGAGCAATGACCTTAAGGAGTGAGCAGCCACCT
TTGGGCTCATCCTGGACAACATGTCATTGGTGTATCAGACCTTTGGGAAGGAGTTCACAGAAGTGGTGAAAACCAAACAG
GTGACTCAGCAGAAAGCAGAAAGGGCCAGATTTGTGGTGGAAAAAGGCTGAGCAGCAAAAAAAGGCAGCCATCATCTCTA
CTGAGGGCAACTCCAAAGCAGCCAAGCTGATTGCCAACTCACTGACCACCACAGGGGATGGCCTGATTGAGCTGCACAAG
CTGGAAGCCATAGAGGACATCGTGTACCAGCTCTCATGCTCTTGGAACCTCACTTACCTGCCAGTGGACAGTCTGTGCTC
CTCCAGCTGCCCCAG

ORF - retro_pabe_289 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.55 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAAKVFESIGKFGLALAVAGGVVNSALYNVDAGHRAVIFDRFRGVQDIVVGEGTHFLIPWVQKPIIFDCR
M.AKVFE.I.KFG..LAVAGGVVNSALYNVDAG.RA.IFD.F.GVQ.IV.G.GT.F.IPW..KPI.FDC.
RetrocopyMTAKVFELISKFGPPLAVAGGVVNSALYNVDAGCRAAIFDQFHGVQNIVAGKGTYFFIPWI*KPITFDCH
Parental-SRPRNVPVITGSKDLQNVNITLRILFRPVASQLPRIFTSIGEDYDERVLPSITTEILKSVVARFDAGEL
.S.PRNVPVITGSKDLQNVNITL.ILF...ASQLP.I.TSIG.DYDERVL.SIT.EIL.SVVA.FDAG.L
Retrocopy<SQPRNVPVITGSKDLQNVNITLHILFWCFASQLPHIYTSIGKDYDERVLLSITIEILRSVVAHFDAGQL
ParentalITQRELVSRQVSDDLTERAATFGLILDDVSLTHLTFGKEFTEAVEAKQVAQQEAERARFVVE-KAEQQKK
ITQRELVSRQVS.DL.E.AATFGLILD..SL...TFGKEFTE.V..KQV.QQ.AERARFVVE.KAEQQKK
RetrocopyITQRELVSRQVSNDLKE*AATFGLILDNMSLVYQTFGKEFTEVVKTKQVTQQKAERARFVVE>KAEQQKK
ParentalAAIISAEGDSKAAELIANSLATAGDGLIELRKLEAAEDIAYQLSRSRNITYLP-AGQSVLLQLPQ
AAIIS.EG.SKAA.LIANSL.T.GDGLIEL.KLEA.EDI.YQLS.S.N.TYLP..GQSVLLQLPQ
RetrocopyAAIISTEGNSKAAKLIANSLTTTGDGLIELHKLEAIEDIVYQLSCSWNLTYLP<SGQSVLLQLPQ

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 84 .54 RPM
SRP007412_cerebellum 0 .00 RPM 38 .79 RPM
SRP007412_heart 0 .00 RPM 81 .52 RPM
SRP007412_kidney 0 .00 RPM 193 .51 RPM
SRP007412_liver 0 .00 RPM 78 .40 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_289 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_289 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_289 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_521

Parental genes homology:
Parental genes homology involve 16 parental genes, and 123 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000047971 retrocopy
Canis familiaris ENSCAFG000000169261 retrocopy
Choloepus hoffmanni ENSCHOG000000075882 retrocopies
Callithrix jacchus ENSCJAG0000000717422 retrocopies
Erinaceus europaeus ENSEEUG000000064813 retrocopies
Homo sapiens ENSG0000016708515 retrocopies
Gorilla gorilla ENSGGOG0000002800212 retrocopies
Macropus eugenii ENSMEUG000000051221 retrocopy
Myotis lucifugus ENSMLUG000000082032 retrocopies
Macaca mulatta ENSMMUG0000000015613 retrocopies
Monodelphis domestica ENSMODG000000122101 retrocopy
Otolemur garnettii ENSOGAG000000270151 retrocopy
Procavia capensis ENSPCAG000000088511 retrocopy
Pongo abelii ENSPPYG00000008920 16 retrocopies
Pan troglodytes ENSPTRG0000000937614 retrocopies
Rattus norvegicus ENSRNOG0000004679918 retrocopies



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