RetrogeneDB ID:

retro_rnor_981

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:13:98205012..98206336(-)
Located in intron of:ENSRNOG00000003778
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Chm
Ensembl ID:ENSRNOG00000000161
Aliases:None
Description:rab proteins geranylgeranyltransferase component A 1 [Source:RefSeq peptide;Acc:NP_058763]


Retrocopy-Parental alignment summary:






>retro_rnor_981
AACCGGGATGCACACAGTTTCAGATGGAGAAGAAGGTGAACACAAACTTGCTGCAGAAGACAACGTAGGACAACCAAAGA
GAAATACGATTACTTACTCGCAGATGGTCAAGGAGAGCCGGACATTCAACATTGACTTGGTATCAAAGCTGCTGTATTCT
CAAGGCTCACTGATCGATCTTCTAATCAAATCAAACGTTAGTCGTTATGCAGAGTTTAAGAATGTTACTAGGATCCTTGC
ATTTCGGGAAGGGAAGGTAGAACAGGTGCCTTGCTCCAGAGCAGATGTGTTTAACAGTAAAGAGCTCACTATGGTTGAGA
AGAGAATGCTAATGAAGTTTCTCACGTTCTGTTTAGACTACGAGCAACATTCAGATGAATACCAAGATTTCAAACAATGT
TCATTTTCTGACTACTTAAAAACTAAAAAGCTAACGCCTAACCTCCAACACTTCATACTCCACTCAATTGCAATGTCGTC
AGACTCATCCTGCACTACATTAGATGGCCTTCAAGCAACAAAGAACTTCCTTCGGTGTCTTGGACGGTTTGGCAACACTC
CCTTTATATTCCCTTTATACGGCCAAGGAGAAATTCCCCAGTGTTTCTGCAGGATGTGCGCAGTTTTTGGTGGAGTCTAT
TGCCTTCGCCATAAGGTACAATGTCTTGTAGTTGACAGAGACTCTGGAAGATGTAAAGGAATCATAGATGGCTTTGGGCA
GAGAATAAGTGCCAACTATTTTATCGTGGAGGACAGTTACCTTTCTAAGGAAATGTGTTCAAACATTCAGTATAAGCAGA
TCTCAAGGGCAGTGCTTATCACAGATCAGTCCATCCTGAAGACTGATTCAGACCAGCAGATTTCCATTTTGGTAGTGCCT
CCTCTGGAGCCGGGAACTGCTTCGGTTCGGGTCATGGAATTATGTTCCTCAACCATGACATGCATGAAGGACAGCTATCT
GGTCCACTTGACCTGTTTCTCTTCAAAAACAGCCCGAGAAGACTTGGAACCCGTGGTGAAGCAGTTATTCATCCCTTTTG
CAGAAGCAGAAGCAGACAAAGAGGAACTCAGAAAACCAAGACTTTTGTGGGCCCTTTATTTTAATATGAGAGATTCCTCA
GGGGTGAGCCGAAGCTCATACTGTAGCTTACCTTCCAATGTATACATCTGCTCTGGTCCTGACTGTGGACTGGGGAATGA
GCATGCAGTCAAGCAAGCGGAAACACTGTTCCAGGAGATCTTTCCCAGTGAAGAGTTCTGCCCTCCTCCACCAAACCCTG
AAGACATTATCTTTGAAGCGGAGGGTTAGCAACCAGACACTCCT

ORF - retro_rnor_981 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.49 %
Parental protein coverage: 68.16 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalNSDAKS-STEEPSENVPKVQDNTETPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRY
N.DA.S.S..E..E......DN...PK.N.ITYSQ..KE.R.FNIDLVSKLLYS.G.LIDLLIKSNVSRY
RetrocopyNRDAHS>SDGEEGEHKLAAEDNVGQPKRNTITYSQMVKESRTFNIDLVSKLLYSQGSLIDLLIKSNVSRY
ParentalAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVEYEEHPDEYRAYEGTTFSEYL
AEFKN.TRILAFREG.VEQVPCSRADVFNSK.LTMVEKRMLMKFLTFC..YE.H.DEY.......FS.YL
RetrocopyAEFKNVTRILAFREGKVEQVPCSRADVFNSKELTMVEKRMLMKFLTFCLDYEQHSDEYQDFKQCSFSDYL
ParentalKTQKLTPNLQYFVLHSIAMTSETTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVF
KT.KLTPNLQ.F.LHSIAM.S.....T.DGL.ATK.FL.CLGR.GNTPF.FPLYGQGE.PQCFCRMCAVF
RetrocopyKTKKLTPNLQHFILHSIAMSSDSSCTTLDGLQATKNFLRCLGRFGNTPFIFPLYGQGEIPQCFCRMCAVF
ParentalGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSYLSENTCSRVQYRQISRAVLITDGSVL
GG.YCLRH.VQCLVVD..S..CK..ID.FGQRI....FI.EDSYLS...CS..QY.QISRAVLITD.S.L
RetrocopyGGVYCLRHKVQCLVVDRDSGRCKGIIDGFGQRISANYFIVEDSYLSKEMCSNIQYKQISRAVLITDQSIL
ParentalKTDADQQVSILTVPAEEPGSFAVRVIELCSSTMTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEI
KTD.DQQ.SIL.VP..EPG...VRV.ELCSSTMTCMK..YLVHLTC.SSKTAREDLE.VV..LF.P..E.
RetrocopyKTDSDQQISILVVPPLEPGTASVRVMELCSSTMTCMKDSYLVHLTCFSSKTAREDLEPVVKQLFIPFAEA
ParentalEAENEQVEKPRLLWALYFNMRDSSDISRDCYNDLPSNVYVCSGPDSGLGNDNAVKQAETLFQQICPNEDF
EA..E...KPRLLWALYFNMRDSS..SR..Y..LPSNVY.CSGPD.GLGN..AVKQAETLFQ.I.P.E.F
RetrocopyEADKEELRKPRLLWALYFNMRDSSGVSRSSYCSLPSNVYICSGPDCGLGNEHAVKQAETLFQEIFPSEEF
ParentalCPAPPNPEDIVLDGDSSQQEVP
CP.PPNPEDI.......Q...P
RetrocopyCPPPPNPEDIIFEAEG*QPDTP

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 3 .95 RPM 22 .50 RPM
SRP017611_kidney 2 .09 RPM 25 .05 RPM
SRP017611_liver 0 .27 RPM 7 .06 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_981 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_981 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_981 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
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 ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG00000000161 1 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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