RetrogeneDB ID:

retro_pabe_215

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:7619282..7621208(+)
Located in intron of:ENSPPYG00000000069
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSPPYG00000020520
Aliases:None
Description:rab proteins geranylgeranyltransferase component A 1 [Source:RefSeq peptide;Acc:NP_001124994]


Retrocopy-Parental alignment summary:






>retro_pabe_215
GTGGTTATAATAGGGACAGGTTTGCCTGAATCCATCCTTGCAGCTGCATGTTCAAGAAGTGGTCAGAGGGTTCTGCATAT
TGATTCAAGAAGTTACTATGGAGGAAACTGGGCTAGTTTCAGCTTTTCAGGATTGCTATCCTGGTTGAAGGAGTATCAGC
AAAACAATGACACTGGGGAAGAAAGTACTGTTGCATGGCAGGACCTGATCCATGAAACAGAAGAAGCCATCACTCTTCGC
AAGAAGGATGAAACTATTCAACACACAGAAGCTTTTTGCTACGCCAGTCAGGATATGGAGGACAACGTTGAAGAGATTGG
TGCTCTGCAGAAAAATCCTTCTTCGGGGGTGTCTAATAACTTCACTGAAGTTTTGGATTCTGCATTGCCCGAAGAAAGCC
AGTCATCATATTTTGATAGCGACGAAATGCCTGCCAAACACACTCAGAAAAGTGATACAGAGATTTCACTAGAAGTAACT
GATGTAGAGGAATCAGTGGAGAAGGAAAAGTATTGTGGAGATAAAACTTGTATGCACACAGTTTCAGATAAAGATGGAGA
TAAAGATGAAAACAAATCTACAGTAGAAGATAATGCCGATGAACCAATTAGAAATAGGATTACTTACTCTCAAATAGTTA
AAGAAGGCAGGAGGTTTAATATTGATTTGGTATCAAAACTGCTGTATTCTCAAGGATTGCTAATTGATCTTTTAATCAAA
TCAGATGTTAGTCGTTATGTAGAATTTAAAAATGTCACTAGGATTCTTGCATTTCGGGAAGGAAAGGTAGAACAAGTGCC
TTGTTCCAGAGCAGATGTCTTTAATAGCAAGGAACTCACCATGGTTGAAAAGAGGATGCTAATGAAATTTCTCACATTTT
GTTTAGAGTATGAACAACGTCCTGATGAATACCAAGCTTTCAGGCAGTGTTCATTTTCAGAATATTTAAAAACTAAAAAA
CTAACTCCCAACCTTCAACATTTTGTTCTGCACTCAATTGCAATGACATCAGAATCTTCCTGCACTACAATAGATGGTCT
TAACGCAACTAAAAACTTCCTTCAGTGTCTCGGACGGTTTGGCAACACTCCGTTTTTATTTCCCTTGTATGGCCAAGGAG
AAATTCCCCAGGGTTTCTGTAGGATGTGTGCAGTTTTTGGTGGAATCTATTGTCTTCGTCATAAAGTACAATGCTTTGTA
GTCGACAAAGAATCTGGACGATGTAAAGCAATTATAGATAACTTTGGTCAAAGAATAAATGCTAAATATTTTATTGTGGA
AGACAGTTACCTTTCTGAGGAAACATGCTCAAATGTGCAGTATAAGCAGATCTCTAGGGCAGTACTCATTACAGATCAGT
CTATACTAAAGACAGATTCAGATCAGCAGACTTCCATTCTGATAGTTCCTCCCACAGAGCCAGGAGCTTGGGCTGTACGG
GTCACAGAATTATGTTCTTCAACCATGACATGCATGAAGGACACCTATCTGGTACATTTGACATGTTCATCTTCTAAAAC
AGCAAGAGAAGACTTAGAATCAGTGGTGAAGAAATTATTCACTCCGTATACTGAAACAGAAATAAACGAGGAAGAACTTA
CAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCCTCGGGAATCAGCAGAAGCTCATATAATGGCTTG
CCTTCCAATGTTTATGTCTGCTCTGGGCCTGACTGTGGCCTGGGAAATGAGCATGCTGTCAAGCAAGCTGAAACACTTTT
CCAGGAGATCTTTCCAACTGAAGAATTCTGCCCTCCACCTCCAAATCCAGAAGACATTATCTTTGATGGTGATGATAAGC
AGCCAGACGCTCCTGGAACCAATAATATAATAATGGCCAAACTAGAATCCTCTGATGAAAGCAAAAACCTAGAAAGCCCA
GAGAAG

ORF - retro_pabe_215 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.38 %
Parental protein coverage: 99.38 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLIVIGTGLPESITAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENSDIVSDSPV-WQDQI
...IGTGLPESI.AAACSRSG.RVLH.DSRSYYGGNWASFSFSGLLSWLKEYQ.N.D....S.V.WQD.I
RetrocopyVVIIGTGLPESILAAACSRSGQRVLHIDSRSYYGGNWASFSFSGLLSWLKEYQQNNDTGEESTVAWQDLI
ParentalLENEEAIALSRKDKTIQHVEVFCYASQDLNEDVEEAGALQKNHALVTSANSTEASDSAFLPTEDESLSTM
.E.EEAI.L..KD.TIQH.E.FCYASQD....VEE.GALQKN.....S.N.TE..DSA.LP.E..S....
RetrocopyHETEEAITLRKKDETIQHTEAFCYASQDMEDNVEEIGALQKNPSSGVSNNFTEVLDSA-LPEESQSSYFD
ParentalSCEMLTEQTPSSDPENALEVNGAEVTGEKENHCDDKTCVPSTSAED--MSENVPIAEDTTEQPKKNIITY
S.EM....T..SD.E..LEV...E...EKE..C.DKTC....S..D....EN....ED....P..N.ITY
RetrocopySDEMPAKHTQKSDTEISLEVTDVEESVEKEKYCGDKTCMHTVSDKDGDKDENKSTVEDNADEPIRNRITY
ParentalSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGQVEQVPCSRADVFNSKQL
SQI.KEGRRFNIDLVSKLLYS.GLLIDLLIKS.VSRY.EFKN.TRILAFREG.VEQVPCSRADVFNSK.L
RetrocopySQIVKEGRRFNIDLVSKLLYSQGLLIDLLIKSDVSRYVEFKNVTRILAFREGKVEQVPCSRADVFNSKEL
ParentalTMVEKRMLMKFLTFCMEYEKYPDEYKGYEEITFYEYLKTQKLTPNLQYIVLHSIAMTSETTSSTMDGLKA
TMVEKRMLMKFLTFC.EYE..PDEY.......F.EYLKT.KLTPNLQ..VLHSIAMTSE....T.DGL.A
RetrocopyTMVEKRMLMKFLTFCLEYEQRPDEYQAFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLNA
ParentalTKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAIIDQFGQRI
TKNFL.CLGR.GNTPFLFPLYGQGE.PQ.FCRMCAVFGGIYCLRH.VQC.VVDKES..CKAIID.FGQRI
RetrocopyTKNFLQCLGRFGNTPFLFPLYGQGEIPQGFCRMCAVFGGIYCLRHKVQCFVVDKESGRCKAIIDNFGQRI
ParentalISEHFLVEDSYFSENMCSRVQYRQISRAVLITDRSVLKTDSDQQISILTVPAEEPGTFAVRVIELCSSTM
....F.VEDSY.SE..CS.VQY.QISRAVLITD.S.LKTDSDQQ.SIL.VP..EPG..AVRV.ELCSSTM
RetrocopyNAKYFIVEDSYLSEETCSNVQYKQISRAVLITDQSILKTDSDQQTSILIVPPTEPGAWAVRVTELCSSTM
ParentalTCMKGTYLVHLTCTSSKTAREDLEPVVQKLFIPYTEMEIENEQVEKPRILWALYFNMRDSSDISRSCYSD
TCMK.TYLVHLTC.SSKTAREDLE.VV.KLF.PYTE.EI..E...KPR.LWALYFNMRDSS.ISRS.Y..
RetrocopyTCMKDTYLVHLTCSSSKTAREDLESVVKKLFTPYTETEINEEELTKPRLLWALYFNMRDSSGISRSSYNG
ParentalLPSNVYVCSGPDCGLGNDNAVKQAETLFQEICPNEDFCPPPPNPEDIVLDGDGLQPETSESSAIPEANSE
LPSNVYVCSGPDCGLGN..AVKQAETLFQEI.P.E.FCPPPPNPEDI..DGD..QP.......I..A..E
RetrocopyLPSNVYVCSGPDCGLGNEHAVKQAETLFQEIFPTEEFCPPPPNPEDIIFDGDDKQPDAPGTNNIIMAKLE
ParentalTFEESTNLGNLEE
...ES.NL...E.
RetrocopySSDESKNLESPEK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 7 .24 RPM 21 .23 RPM
SRP007412_cerebellum 2 .43 RPM 22 .50 RPM
SRP007412_heart 3 .58 RPM 5 .75 RPM
SRP007412_kidney 2 .65 RPM 8 .92 RPM
SRP007412_liver 2 .39 RPM 4 .65 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_215 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_215 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_215 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_56
Pan troglodytes retro_ptro_400
Gorilla gorilla retro_ggor_488
Macaca mulatta retro_mmul_460
Mus musculus retro_mmus_284
Rattus norvegicus retro_rnor_981
Oryctolagus cuniculus retro_ocun_893
Bos taurus retro_btau_227
Canis familiaris retro_cfam_1873
Equus caballus retro_ecab_36
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG00000020520 1 retrocopy
retro_pabe_215 ,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


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