RetrogeneDB ID:

retro_cfam_1873

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:7:33034340..33036290(-)
Located in intron of:ENSCAFG00000015729
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSCAFG00000017406
Aliases:None
Description:choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940]


Retrocopy-Parental alignment summary:






>retro_cfam_1873
ATGGCGGACAGTCTTCCCACAGAGTTCGATGTGGTCATAATAGGGACAGGTCTACCTGAATCCATCCTGGCAGCTGCATG
TTCAAGAAGTGGTCAGAGAGTTCTTCATCTTGATTCAAGAAGTTACTATGGAGGAAACTGGGCAAGTTTCAGCTTTTCGG
GATTGCTCTCCTGGTTAAAGGAGCATCAGCAAAACGGTGACAATGCAGAAGAAAGCACTGCTTCATGGCAAGGCCTGGTG
CATGAAACAGAAGAAGCCATTGCTCTTCGCAAGAAGGATGAAACCATTGAACACATAGAAGTTTTCTGTTATGCCAGTCA
GGATATGGATGACAATATTGAAGAGATCAGTGCTCTGCAGAAAAATCCTTCCGCAGTAACATCTAAACCTCTGGATTCTG
TGTGCTTGTCCGAAGAAACAAACTCATTACATGTTACTAGCTCTGAAACGCATGCCAAAGACACTCCAAAAAGTGATGAA
GAGATTTCACTGGAAGTAACTGATGTAGAGGACATCTTGGCAGAAGAAAAATGTTGTGGAGATAAAACCTGTATAAACAC
AGCTTCAGGTGGAGATAAAGATGAAAACAAACCTATAGAGGAAGATAACACTGATCAACCAAAGAGAAATAGGATTACTT
ACTCTCAAATAGTTAAAGAAGGCAGGAGATTTAATATTGATTTGGTATCAAAGCTGCTGTATTCTCAAGGATTGCTAATC
GATCTTTTAATCAAATCAAATGTTAGTCGTTATGCAGAATTTAAAAACGTCACTAGGATTCTTGCATTTCGCGAGGGAAA
AGTAGAACAGGTGCCTTGTTCCAGAGCAGATGTCTTTAATAGCAAAGAACTCACTATGGTTGAAAAGAGGATACTGATGA
AATTTCTTACATTTTGTTTAGACTATGAACAACATCCTGATCAATACCAAGCTTTTGTGCATTGCTCATTTTCAGATTAC
TTAAAAACTAAAAAATTAACCCCCAACCTCCAACATTTTGTGCTGCACTCAATTGCAATGACAGAGTCCTCTTGCACCAC
AATAGATGGCCTTAAAGCAACTAAAAACTTCCTTCGGTGTCTTGGACGGTTTGGCAACACTCCCTTTTTATTTCCCTTGT
ATGGCCAAGGAGAAATTCCCCAGTGTTTCTGCAGGATGTGTGCAGTTTTTGGTGGAATCTATTGTCTTCGCCATAAAGTT
CAATGCCTTATAGTTGACAAAGAATCTGGAAGATGTAAAGCAATTATAGATCACTTAGATCAAAGAATAAATGCTAAATA
TTTTATTGTGGAGGATAGTTACCTTTCTGAGGAAACATGCTCAAATGTGCAATATAAGCAGATCTCCAGGGCAGTGCTCA
TTACAGATCAGTCTATACTCAAGAAGGCAGATTCAGATCAGCAAATTTCCATTTTGATAGTGCCTCCAATGGAATCAGGA
ACATGTGCTGTTCGTGTCACTGAATTATGTTCTTCAACCATGACATGCATGAAAGACACCTATCTGGTACATCTGACCTG
TTCATCTTCTAAAACAGCAAGAGAAGACTTAGAGTCAGTAGTGAAGAAATTATTCACCCCATATACTGAAACAGAAATAG
ACAAGGAAGAACTCACAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCCTCGGGAATCAGCAGAAGC
TCATACAATGGCTTACCTTCCAATGTTTATGTCTGCTCTGGGCCTGACTGCGGACTGGGAAATGAGCACGCAGTCAAGCA
AGCTGAAACACTTTTCCAGGAGATCTTTCCCAATGAAGACTTCTGCCCCCCACCTCCAAATCCAGAAGATATAATCTTTG
ATGGTGATGATAAGCAACCTGAGGCTCTTGGAACCAATAATATAATCATGGCCAAACCAGACTACTCTGAGGAAAATAAA
AACCCAGAAAGCCCAGAGAACCACCTTCAA

ORF - retro_cfam_1873 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.69 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADNLPSEFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGILSWLKEYQENSDIVN
MAD.LP.EFDV..IGTGLPESI.AAACSRSGQRVLH.DSRSYYGGNWASFSFSG.LSWLKE.Q.N.D...
RetrocopyMADSLPTEFDVVIIGTGLPESILAAACSRSGQRVLHLDSRSYYGGNWASFSFSGLLSWLKEHQQNGDNAE
ParentalEGPA-WQEQILENEEAIALSRKDKTIQHVEVFCYASQDLHEEVEEAGALQKNHASVISENPTEAVHSAYL
E..A.WQ....E.EEAIAL..KD.TI.H.EVFCYASQD.....EE..ALQKN...V.S........S..L
RetrocopyESTASWQGLVHETEEAIALRKKDETIEHIEVFCYASQDMDDNIEEISALQKNPSAVTSK----PLDSVCL
ParentalPSEDESLCIASCEMLTEQTPSSDLETALEISNVK-VTGETEKHDDKTCMKSASEEETSKNVPTTEGTALQ
..E..SL...S.E.....TP.SD.E..LE...V.....E.....DKTC...AS......N.P..E....Q
RetrocopySEETNSLHVTSSETHAKDTPKSDEEISLEVTDVEDILAEEKCCGDKTCINTASGGDKDENKPIEEDNTDQ
ParentalPKKTRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGRVEQVPCSRA
PK..RITYSQI.KEGRRFNIDLVSKLLYS.GLLIDLLIKSNVSRYAEFKN.TRILAFREG.VEQVPCSRA
RetrocopyPKRNRITYSQIVKEGRRFNIDLVSKLLYSQGLLIDLLIKSNVSRYAEFKNVTRILAFREGKVEQVPCSRA
ParentalDVFNSKQLTMVEKRMLMKFLTFCMEYEKHPDEYKAYEEITFSEYLKTQKLTPNLQYFVLHSIAMTSETAS
DVFNSK.LTMVEKR.LMKFLTFC..YE.HPD.Y.A.....FS.YLKT.KLTPNLQ.FVLHSIAMT.E...
RetrocopyDVFNSKELTMVEKRILMKFLTFCLDYEQHPDQYQAFVHCSFSDYLKTKKLTPNLQHFVLHSIAMT-ESSC
ParentalNTIDGLKATKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAI
.TIDGLKATKNFL.CLGR.GNTPFLFPLYGQGE.PQCFCRMCAVFGGIYCLRH.VQCL.VDKES..CKAI
RetrocopyTTIDGLKATKNFLRCLGRFGNTPFLFPLYGQGEIPQCFCRMCAVFGGIYCLRHKVQCLIVDKESGRCKAI
ParentalIDQFGQRIISKHFLVEDSYFSENTCSHVQYRQISRSVLITDRSVLK-TDSDQQISILTVPGEEPGTFAVR
ID...QRI..K.F.VEDSY.SE.TCS.VQY.QISR.VLITD.S.LK..DSDQQISIL.VP..E.GT.AVR
RetrocopyIDHLDQRINAKYFIVEDSYLSEETCSNVQYKQISRAVLITDQSILKKADSDQQISILIVPPMESGTCAVR
ParentalVIELCSSTMTCMKGTYLVHLTCTSSKTAREDLEPVVQKLFTPYTETETENEEVEKPRLLWALYFNMRDSS
V.ELCSSTMTCMK.TYLVHLTC.SSKTAREDLE.VV.KLFTPYTETE...EE..KPRLLWALYFNMRDSS
RetrocopyVTELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLFTPYTETEIDKEELTKPRLLWALYFNMRDSS
ParentalDVSRNSYNDLPSNVYVCSGPDSGLGNDNAVKQAETLFQLICPNEDFCPPPPNPEDIITDGDSLQSEASEA
..SR.SYN.LPSNVYVCSGPD.GLGN..AVKQAETLFQ.I.PNEDFCPPPPNPEDII.DGD..Q.EA...
RetrocopyGISRSSYNGLPSNVYVCSGPDCGLGNEHAVKQAETLFQEIFPNEDFCPPPPNPEDIIFDGDDKQPEALGT
ParentalSVILEANSETPKESASLGNPEEASQ
..I..A......E......PE...Q
RetrocopyNNIIMAKPDYSEENKNPESPENHLQ

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
SRP012049_cerebellum 29 .36 RPM 41 .12 RPM
SRP017611_brain 76 .69 RPM 29 .69 RPM
SRP017611_kidney 16 .31 RPM 24 .24 RPM
SRP017611_liver 14 .72 RPM 6 .96 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1873 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1873 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1873 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
Oryctolagus cuniculus retro_ocun_893
Bos taurus retro_btau_227
Equus caballus retro_ecab_36
Parental genes homology:
Parental genes homology involve 22 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000052232 retrocopies
retro_cfam_2196, retro_cfam_886,
Canis familiaris ENSCAFG00000017406 1 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 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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