RetrogeneDB ID:

retro_btau_227

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:16:35948786..35950742(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000010803
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSBTAG00000009598
Aliases:None
Description:rab proteins geranylgeranyltransferase component A 1 [Source:RefSeq peptide;Acc:NP_001192318]


Retrocopy-Parental alignment summary:






>retro_btau_227
ATGGCCAACAGTCTCCCAACAGAATTTGATGTGATAGTGATGGGGACAGGTCTGCCTGAATCCATCCTTGCCGCTGCATG
TTCCAGAAGTGGTCAAAGGGTTCTGCATCTCGATTCAAGAAGTTACTATGGGGGAAACTGGGCTAGTTTCAGCTTTCCAG
GATTGCTATCCTGGTTGAAGGAACATCAGCAAAACAGTGACACTGGGGAGGAAAGCCCTGCTGCATGGCAAGACATGATC
CATGAAACAGAAGAAGCCATCCCTCTTTGCAAGAAGGATGAAACCATTCAACACGCCGAAGTTTTTTGTTATGCCAGTCA
GGGCATGGATGGCAATATTGAAGAGCTTGGTGCCCTGCAGAAAAATCCTTCTTGTGTAGCATCTAGTACCCTCATAAAAC
CTCTGGATTCTGCATGCTTGTCTGAGGAAACACACTCATCACACATTACTAGCTATGAAGTGCCTACACAAGACACTCCA
AAAAACAATGAAGAAATAACTGATACGGCAGAAACTTCTGTGAAAGAAGAATATTGTGGGTATGATACTTATAAACACAC
AGTTTCAGATGGCACTAAAGATGAAATCAAACCTGTACTGGAAGACAACAGTGTGCCACCAAAGAGAAAAAGGATTGCTT
ACTCTCAAATAGTTAAAGAAGGCAGGAGGTTTAATATTGATCTGTCATCGAAGCTGCTTTATTCTCAAGGACTGTTAATC
GATCTGTTAATCAAATCAAATGTTAGTCGTTACGCTGAATTTAAAAATGTCACTAGAATTCTTGCATTTCGAGAAGGAAA
AGTAGAGCAGGTGCCTTGTTCCAGAGCAGATGTCTTTAATAGCAAAGAGCTCACTATGGTTGAAAAGAGGATGCTAATGA
AATTTCTTACATTTTGTTTAGATTATGAACAACATCCTGAGGAATACCAAGCTTTCACACAATGCTCATTTTCAGAGTAC
TTGAAAACCAAAAACTTAACCCCCAGCCTCCAGCATTTTATACTTCACTCGATTGCCATGATGTCAGAATCCTCTTGCAC
TACAGTAGATGGCCTTAAAGCAACAAAAACCTTTCTTCAGTGTCTTGGACGGTTTGGCAACACTCCCTTTTTATTTCCCT
TATATGGCCAAGGTGAAATTCCCCAGTGTTTCTGCAGGATGTGTGCAGTTTTCGGTGGGATATATTGTCTTCGCCATAAA
GTACAATGCCTTGTAGTTGACAGAGAATCTGGAAGATGTAAAGCAATTATAGATCACCTTGGTCAAAGGATAAATGCTAA
ATATTTCATTGTGGAAGATAGTTACCTGTCTGAGGAAACATGTTCAAGTGTGCAGTACAAGCAGATATCCAGGGCAGTGC
TCATTACAGATCAGTCTGTCCTAAAGACAGATTCAGATCAGCAGATTTCCATTTTGATAGTACCTCCGGTGGAACCAGGA
GCACATGCTGTCCGAATCATTGAATTGTGTTCTTCAACCATGACATGCATGAAAGACACCTACCTGGTACATCTGACCTG
TTCATCTTCCAAAACAGCAAGAGAAGACTTAGAATCAGTGGTGAAGAAATTATTCACCCCATATTCTGAGACAGAAGTAG
ACAATGAAGAACTTCCAAAGCCAGGACTCTTGTGGGCTCTTTATTTTAACATGAGAGATTCCTCGGGAGTCAGCCGTAGC
TCATACAATGGCTTGCCTCCCAACGTTTATGTCTGCACTGGGCCTGACTCTGGACTCGGAAGTGAGCATGCCGTCAAGCA
AGCTGAAACACTCTTCCACGAGATCTTTCCAAGTGAAGAATTCTGCCCCCCACCTCCAAATCCGGAAGACATTTTCTTTG
ACGGTGATGAAAAGCCATCAGAGCCTCTTGGAACCAATAATATAGTAATGGCCAAACTAGAATCCTCTGAGGGAAGCAAA
AACCTAGAAAGTTCAGGGAAGCACCTTCAAAATTAG

ORF - retro_btau_227 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.65 %
Parental protein coverage: 99.02 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRSYYGGNWASFSFSGLLSWLKEHQENSDIVNECPA-WQEKIHENEEAIALSRTDKTIQHVEVFCYACQDL
RSYYGGNWASFSF.GLLSWLKEHQ.NSD...E.PA.WQ..IHE.EEAI.L...D.TIQH.EVFCYA.Q..
RetrocopyRSYYGGNWASFSFPGLLSWLKEHQQNSDTGEESPAAWQDMIHETEEAIPLCKKDETIQHAEVFCYASQGM
ParentalHEDVEEAGALQKNHASVTSVNCTEAADSACLPVEDESLRTTSCEIPAEQTPSSDPERALEVNDVQVTGEK
....EE.GALQKN...V.S.......DSACL..E..S...TS.E.P...T....P....E..D...T..K
RetrocopyDGNIEELGALQKNPSCVASSTLIKPLDSACLSEETHSSHITSYEVPTQDT----PKNNEEITDTAETSVK
ParentalENCCDDNTCVPSTAEKETSENVPVAEDTAEQPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIK
E..C...T...........E..PV.ED....PK..RI.YSQI.KEGRRFNIDL.SKLLYS.GLLIDLLIK
RetrocopyEEYCGYDTYKHTVSDGTKDEIKPVLEDNSVPPKRKRIAYSQIVKEGRRFNIDLSSKLLYSQGLLIDLLIK
ParentalSNVSRYAEFKNITRILAFREGRVKQVPCSRADVFNSKQLTMVEKRMLMKFLTFCMEYEEHPDEYKAYEEI
SNVSRYAEFKN.TRILAFREG.V.QVPCSRADVFNSK.LTMVEKRMLMKFLTFC..YE.HP.EY.A....
RetrocopySNVSRYAEFKNVTRILAFREGKVEQVPCSRADVFNSKELTMVEKRMLMKFLTFCLDYEQHPEEYQAFTQC
ParentalTFSEYLKTQKLTPNLQYFVLHSMAMTSETGSSTIDGLKATKNFLHSLGRYGNTPFLFPLYGQGELPQCFC
.FSEYLKT..LTP.LQ.F.LHS.AM.SE....T.DGLKATK.FL..LGR.GNTPFLFPLYGQGE.PQCFC
RetrocopySFSEYLKTKNLTPSLQHFILHSIAMMSESSCTTVDGLKATKTFLQCLGRFGNTPFLFPLYGQGEIPQCFC
ParentalRMCAVFGGIYCLRHSVQCLVVDKESGKCKAIIDQYGQRIISKHFLVEDSYLSENTCAHVQYRQISRAILI
RMCAVFGGIYCLRH.VQCLVVD.ESG.CKAIID..GQRI..K.F.VEDSYLSE.TC..VQY.QISRA.LI
RetrocopyRMCAVFGGIYCLRHKVQCLVVDRESGRCKAIIDHLGQRINAKYFIVEDSYLSEETCSSVQYKQISRAVLI
ParentalTDRSVLKTDSDQQISILTVPAEEPGTFAVRVIELCSSTMTCMKGSYLVHLTCTSSKTAREDLEPVVQKLF
TD.SVLKTDSDQQISIL.VP..EPG..AVR.IELCSSTMTCMK..YLVHLTC.SSKTAREDLE.VV.KLF
RetrocopyTDQSVLKTDSDQQISILIVPPVEPGAHAVRIIELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLF
ParentalTPYTETEIENEEIEKPRLLWGLYFNMRDSSDVNRNTYNDLPSNVYVCSGPDCALGNDNAVKQAEALFQQI
TPY.ETE..NEE..KP.LLW.LYFNMRDSS.V.R..YN.LP.NVYVC.GPD..LG...AVKQAE.LF..I
RetrocopyTPYSETEVDNEELPKPGLLWALYFNMRDSSGVSRSSYNGLPPNVYVCTGPDSGLGSEHAVKQAETLFHEI
ParentalCPNEDFCPPPPNPEDIILDGDSLQPEASESSALPEASSETPKESSNLRN
.P.E.FCPPPPNPEDI..DGD....E.........A..E....S.NL..
RetrocopyFPSEEFCPPPPNPEDIFFDGDEKPSEPLGTNNIVMAKLESSEGSKNLES

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
ERP005899_liver 3 .46 RPM 1 .66 RPM
ERP005899_muscle 7 .92 RPM 5 .12 RPM
SRP017611_brain 12 .15 RPM 7 .31 RPM
SRP017611_kidney 15 .35 RPM 8 .89 RPM
SRP017611_liver 8 .76 RPM 2 .64 RPM
SRP030211_testis 2 .37 RPM 0 .83 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_btau_227 retrocopy
EST ID Start End Identity Match Mis-match Score
BI539416 35950407 35950577 97.7 169 0 166

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_227 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_227 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
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 ENSBTAG000000053161 retrocopy
retro_btau_1208,
Bos taurus ENSBTAG00000009598 1 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 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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