RetrogeneDB ID:

retro_ocun_893

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:16:31559953..31561900(-)
Located in intron of:ENSOCUG00000007707
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSOCUG00000012819
Aliases:None
Description:choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940]


Retrocopy-Parental alignment summary:






>retro_ocun_893
ATGGCGCACAGTCTCCCCACAGAGTTTGATGTGGTTGTAATAGGGACAGGTTTGCCAGAGTCTATCCTTGCAGCTGCATG
TGCAAGAAGTGGTCAGAGGGTTCTGCATCTTGATTCAAGAAGTTATTATGGAGGAAACTGGGCTAGTTTCAGCTTTTCTG
GATTACTATCCTGGCTGAATGAGTATCAACAAAACAGTGACATTGGGGAAGAAAGTATTGCTACATGGCAAGACTCAATC
CATGAAACAGAAGAAGCCATCCCTCTTTGCAAGAAGGATAAAAGCATCCAACATACAGAAGTTTTTTGTTACGCCAGTCA
AGATATGGAGGACAGTGTTGAAGACATTGGTGCTGTGCCAAAAAATCCTTCCTCAGCGGCATCTAGTACCCTCACAGAAC
CTCTGAATTCTGCAGCCTTCCCCAAAGAAAGGCACTCATCAGACTTTGCTCACTATGAAATGTCTGCAAAACACACTCAA
AAAAATGAAACAGAGATTTCACTTGAAGTAACTGATATAGAAGAATCACTGGAGAAAGAAAAGTATTGTGGAGACAAAAC
TTCTGCACACACTGTTTCAGATGGAGATGAAGATGAAAACAACCCTAAAGAAGACAATACTGACCAACAAAAGAGAAATA
GGACTACTTATTCTCAAATAATTAAAGAAGAGAGGAGATTTAATATTGATTTGGTGTCAAAGCTGCTATATTCTCAAGGA
TCCTTAATTGATCTTTTAATCAAATCCAATGTTAGTCGTTATGCTGAATTTAAAAATGTCACCAGGATTCTTGCATATCG
GGAAGGGAAGGTGGAACAGGTTCCTTGTTCTAGAGCAGATGTCTTTAATAGCAAAGAACTCACCATGGTTGAAAAGAGGA
TGCTAATGAAATTTCTTACATTCTGTCTAGACTATGAGCAGCATCCTGATGAATACCAAGATTTCAAACAATGTTCATTT
TCAGAGTACTTGAAAGCTAAAAAACTAACCCCCAACCTCCAACATTTTGTGCTACATTCAATTGCAATGACATCAGAAAC
CTCATGTACTACATTAGATGGTCTTAAAGCAACAAAAATTTTTCTTCAGTGTCTTGGACGGTTCGGCAACACTCCCTTTT
TATTTCCTGTGTATGGTCAAGGTGAAATCCCCCAGTGTTTCTGCAGAATGTGTGCAGTTTTTGGTGGAATCTACTGTCTT
CGTCATAAAGTACAGTGTCTTGTAGTTGACAAAGAATCTGGAAGATGTAAAGCCATTATAGATCACTTTGGTCAAAGAAT
AAATGCTAAGTATTTTATCATGGAGGATAGTTACCTTTCTGAGGAAACATGCTCAAATGTGCAGTATAAGCAAATCTCAA
GGGCAGTGCTCATCACAGATCAGTCTCTACTAAAGACAAATTCAGATCAGCAGATTTCCATTTTGATAGTGCCTCCAGTG
GAAGCACAGACTTGTTCTGTCCGGGTCACAGAATTATGTTCTTCAACTATGACATGCATGAAAGACACATATCTGGTACA
TCTAACGTGTCCATCTTCAAAAACGGCACGAGAAGACCTAGAACCAGTGACGCAGAAATTATTCACTCCTTATGCTGAAA
CAGAAATGGAACAGGAAGGGCCTACAAAACCAAGACTCTTATGGGCTCTTTATTTTAACATGAGAGATTCCTCAGTAGTC
AGCAGAGGCTCCTATGATGGCTTACCTTCCAATGTTTATGTCTGCTCTGGGCCTGACTGTGGCCTGGGAAATGAGCATGC
AGTCAAGCAAGCCGAAACACTTTTTCAGGAGATCTTTCCAGGTGAAGAATTCTGCCCTCCACCTCCAAATCCAGAAGACA
TTATCTATGATGGTAATGACAGGCTACTGGAGGCTTCTGGAACCAGTGATACAACAATGGCCAAACAAGAATCCTCTGAG
GACAGCAAAAACTTAGAAAGTCCAGAG

ORF - retro_ocun_893 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.03 %
Parental protein coverage: 99.38 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADNLPSEFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRNYYGGNWASFSFSGLLSWIKEYQENGDTTN
MA..LP.EFDV.VIGTGLPESI.AAAC.RSGQRVLH.DSR.YYGGNWASFSFSGLLSW..EYQ.N.D...
RetrocopyMAHSLPTEFDVVVIGTGLPESILAAACARSGQRVLHLDSRSYYGGNWASFSFSGLLSWLNEYQQNSDIGE
ParentalES-SRWQEQVLENEEAIGLSKKDKTIQHVEVFCYASQDLHEDVEEAGALQKNHASVTSANSTEAADSACL
ES...WQ....E.EEAI.L.KKDK.IQH.EVFCYASQD....VE..GA..KN..S..S...TE...SA..
RetrocopyESIATWQDSIHETEEAIPLCKKDKSIQHTEVFCYASQDMEDSVEDIGAVPKNPSSAASSTLTEPLNSAAF
ParentalPTEDESLSIVSCEMSAEQTPSSDPESAPEVNDAEATGEK----GDHCDDKTSEEETSTNVPTAADTIEQP
P.E..S......EMSA..T.....E...EV.D.E...EK....GD.....T.............D...Q.
RetrocopyPKERHSSDFAHYEMSAKHTQKNETEISLEVTDIEESLEKEKYCGDKTSAHTVSDGDEDENNPKEDNTDQQ
ParentalKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGRVEQVPCSRAD
K.NR.TYSQIIKE.RRFNIDLVSKLLYS.G.LIDLLIKSNVSRYAEFKN.TRILA.REG.VEQVPCSRAD
RetrocopyKRNRTTYSQIIKEERRFNIDLVSKLLYSQGSLIDLLIKSNVSRYAEFKNVTRILAYREGKVEQVPCSRAD
ParentalVFNSKQLSMVEKRMLMKFLTFCMEYEEHPDEYKGYEEIAFSEYLKTQKLTPNLQYFVLHSIAMTSETTTT
VFNSK.L.MVEKRMLMKFLTFC..YE.HPDEY.......FSEYLK..KLTPNLQ.FVLHSIAMTSET..T
RetrocopyVFNSKELTMVEKRMLMKFLTFCLDYEQHPDEYQDFKQCSFSEYLKAKKLTPNLQHFVLHSIAMTSETSCT
ParentalTLDGLKATKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAII
TLDGLKATK.FL.CLGR.GNTPFLFP.YGQGE.PQCFCRMCAVFGGIYCLRH.VQCLVVDKES..CKAII
RetrocopyTLDGLKATKIFLQCLGRFGNTPFLFPVYGQGEIPQCFCRMCAVFGGIYCLRHKVQCLVVDKESGRCKAII
ParentalDQFGQRIMSTHFLVEDSYLSENMCSHVQYRQISRAVLITDRSVLKTDSDQQISILTVPAEEPGTSAVRVI
D.FGQRI....F..EDSYLSE..CS.VQY.QISRAVLITD.S.LKT.SDQQISIL.VP..E..T..VRV.
RetrocopyDHFGQRINAKYFIMEDSYLSEETCSNVQYKQISRAVLITDQSLLKTNSDQQISILIVPPVEAQTCSVRVT
ParentalELCSSTMTCMKGTYLVHLTCTSSKTARDDLEPVVQKLFTPFTEMEIEKEEVEKPRILWALYFNMRDSSDI
ELCSSTMTCMK.TYLVHLTC.SSKTAR.DLEPV.QKLFTP..E.E.E.E...KPR.LWALYFNMRDSS..
RetrocopyELCSSTMTCMKDTYLVHLTCPSSKTAREDLEPVTQKLFTPYAETEMEQEGPTKPRLLWALYFNMRDSSVV
ParentalDRNCYKDLPSNVYVCSGPDCALGNDNAVKQAETLFQQIYPNEDFCPPPPNPEDIILDGDSSQPGASESIA
.R..Y..LPSNVYVCSGPDC.LGN..AVKQAETLFQ.I.P.E.FCPPPPNPEDII.DG......AS....
RetrocopySRGSYDGLPSNVYVCSGPDCGLGNEHAVKQAETLFQEIFPGEEFCPPPPNPEDIIYDGNDRLLEASGTSD
ParentalIPEANSETPEESANLENPQ
...A..E..E.S.NLE.P.
RetrocopyTTMAKQESSEDSKNLESPE

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
SRP017611_brain 12 .47 RPM 51 .93 RPM
SRP017611_kidney 5 .98 RPM 26 .96 RPM
SRP017611_liver 3 .39 RPM 8 .25 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_893 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_893 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_893 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
Pongo abelii retro_pabe_215
Macaca mulatta retro_mmul_460
Mus musculus retro_mmus_284
Rattus norvegicus retro_rnor_981
Bos taurus retro_btau_227
Canis familiaris retro_cfam_1873
Equus caballus retro_ecab_36
Parental genes homology:
Parental genes homology involve 22 parental genes, and 22 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 ENSOCUG000000053671 retrocopy
retro_ocun_69,
Oryctolagus cuniculus ENSOCUG00000012819 1 retrocopy
retro_ocun_893 ,
Pongo abelii ENSPPYG000000205201 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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