RetrogeneDB ID:

retro_pabe_1072

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:13:102399342..102400012(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ADIPOR1
Ensembl ID:ENSPPYG00000000342
Aliases:None
Description:adiponectin receptor 1 [Source:HGNC Symbol;Acc:24040]


Retrocopy-Parental alignment summary:






>retro_pabe_1072
CTACATGGCCATAGACCACCCATGCCTTCCTTTTGGGCTTGCTTCAAGAGCATCTTCCACACCCATGTGGAAACAGGCAA
CATCTGGACCCATCGGCTTGGTTTCATGCTGTTTCTCTTTTGGGGATCTTGACCATGCTCAGACTAAATATGTACTTCAT
GCCCCTCTACAGGAGAAAGTGGTCTGGGGACGTCTTTTGTGGTTATAGTGCTCTGCCTCAGCTCCTCCTGGCTATTCCAC
ACTGTCTATTGTCATTCAGAAGAAAAGTCTCTCAGGCTTTTTCCAAACTAGACTATACAGCAATTGCTCTACTGAATTAC
AGAGGAGCTTTGTCCCCTGCTCTGTTACTCCCACTGTTCCCCACAACCACCAGGCTTCATCTGCCTCTTCTTTGTCTGTG
TTCTGGGGCATTTCTGCCATCATGGTGGCACAGTGGGGACCAATTTCCCACTCCCTAAGCACCAGCAGACACAGCAAGGA
GCATTGCTGGGGACTTAGCTTGAGTGTTACTGTGCCCTGTCATGCATTTTTCCTATCACTGAAGCTTTTGTCAGGGCCAG
CGCCATGGGCTGGATGGGCTGGTCCTTCCTCACCAGCTGTGTTGCACATCACAGGAGCTGGCCTTTATGCTGCTCGAATT
CCTGAATGCTTCTTTCCTGGAAAATTTGAC

ORF - retro_pabe_1072 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.36 %
Parental protein coverage: 58.93 %
Number of stop codons detected: 0
Number of frameshifts detected 12


Retrocopy - Parental Gene Alignment:

ParentalLHGHRPPMPSFRACFKSIFRIHTETGNIWTHLLGFVLFLF-LGILTMLRPNMYFM-APLQEKVVFGMF-F
LHGHRPPMPSF.ACFKSIF..H.ETGNIWTH.LGF.LFLF.LGILTMLR.NMYFM.APLQEKVV.G...F
RetrocopyLHGHRPPMPSFWACFKSIFHTHVETGNIWTHRLGFMLFLF<LGILTMLRLNMYFM<APLQEKVVWGRL<F
ParentalLGAVLCLSFSWLFHTVYCHSEKVS-RTF-SKLDYSGIALL-IMGSFVPWLYYSFYCSPQ-PRLIYLSIVC
...VLCLS.SWLFHTVYCHSE..S.R.F.SKLDY..IALL.I.....P.L.YS..CSPQ.P..I.L..VC
RetrocopyVVIVLCLSSSWLFHTVYCHSEEKSLRLF<SKLDYTAIALL>ITEELCPLLCYS-HCSPQPPGFICLFFVC
ParentalVL-GISAIIVAQW-DRFAT-PKHRQTRAGVFL-GLGLSGVV-PTMHFT-IAEGFVKATTVGQMGWFFLM-
VL.GISAI.VAQW.D.F.T.PKH.QT..G..L.GL.LS..V.P.MHF..I.E.FV.A...G.MGW.FL..
RetrocopyVL>GISAIMVAQW>DQFPT>PKHQQTQQGALL>GLSLSVTV>PVMHFS>ITEAFVRASAMGWMGWSFLT>
ParentalAVMYITGAGLYAARIPERFFPGKFD
AV..ITGAGLYAARIPE.FFPGKFD
RetrocopyAVLHITGAGLYAARIPECFFPGKFD

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 48 .88 RPM
SRP007412_cerebellum 0 .00 RPM 47 .79 RPM
SRP007412_heart 0 .00 RPM 39 .10 RPM
SRP007412_kidney 0 .00 RPM 48 .63 RPM
SRP007412_liver 0 .00 RPM 50 .62 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1072 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1072 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1072 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1322
Callithrix jacchus retro_cjac_504

Parental genes homology:
Parental genes homology involve 20 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000121991 retrocopy
Choloepus hoffmanni ENSCHOG000000064508 retrocopies
Callithrix jacchus ENSCJAG000000062683 retrocopies
Cavia porcellus ENSCPOG000000004821 retrocopy
Dipodomys ordii ENSDORG000000068761 retrocopy
Felis catus ENSFCAG000000135651 retrocopy
Loxodonta africana ENSLAFG000000035201 retrocopy
Macropus eugenii ENSMEUG000000154391 retrocopy
Microcebus murinus ENSMICG000000079423 retrocopies
Myotis lucifugus ENSMLUG000000161022 retrocopies
Macaca mulatta ENSMMUG000000070461 retrocopy
Mustela putorius furoENSMPUG000000112151 retrocopy
Otolemur garnettii ENSOGAG000000338214 retrocopies
Ochotona princeps ENSOPRG000000045283 retrocopies
Pongo abelii ENSPPYG00000000342 1 retrocopy
retro_pabe_1072 ,
Sorex araneus ENSSARG000000076801 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000154593 retrocopies
Tupaia belangeri ENSTBEG000000151492 retrocopies
Tarsius syrichta ENSTSYG000000014911 retrocopy
Tursiops truncatus ENSTTRG000000063812 retrocopies



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