RetrogeneDB ID:

retro_ocun_52

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:15:32505904..32507020(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000003846
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TRAM1
Ensembl ID:ENSOCUG00000008734
Aliases:None
Description:translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]


Retrocopy-Parental alignment summary:






>retro_ocun_52
ATGGGGTTCCGTAAGAAGAGCAGCAAGAACCCCCCGATGCTGAGCCAGGAGTTCATCCTGCAGAATCACGCGGACATCGC
GTCCTGCGTGGGGATGTTCTTCTTGCTGGGGCTTATGTTCGAGGGCACCGCGGGAGTATCGATCGTGTTCCTGACTCTTC
AGCACGGTGTCACGGTCCCTGCGACCGAGGAGCAAGCCTCGGGCTCCAGGTCCCTCTATCACTACGGTGGCAAAGACTTG
GCCACGGTGTTCTTCTACATGCTGGTGGCAATCATTATCCACGCCACCATTCAGGAGTACGTGTTGGATAAAATAAACAA
GAGGATGCAGTTCACCAAAGCGAAACAAAACAAATTTAACGAGTCGGGCCAGTTTAGTGTCTTCTACTTTGTGTCTTGTA
TCTGGGGCACAATCATTCTCATCTCTGAAAACTGCCTGGCAGACCCCACTCTCTTATGGCGCTCTCACCCCCCTAACATG
ATGACATTTCAGATGAAGTTTTTCTACATCTCGCAGTTGGCGTACTGGTTTCACGGTTTTCCTGAACTCTACTTCCAGAA
AATCAGGAAACAGGATATCCCTCGGCAGCTGATCTACATCGGCCTTCACCTCTTTCACATTTCTGGAGCTTACCTTCTGT
ACCTGAATCATCTGGGGCTCCTTCTTTTGGTGCTGCACTACTTTGTTGAGCTACTGTCCCACATGTGCGGCCTGTTTTAT
TTTAGCGACGAAAAGTACCAGAAGGGGCTTTCTCTGTGGGCCCTTGTGTTCATCCTGGGGAGACTGACGACTTTAATCGT
TTCGGTGCTCACTGTTGGGTTTCACCTGGCGGGGTCGCAGACTCGGGATCCAGACGCCCTGACTGGGAACGTGAACGTGT
TGGCCGCTAAAATCGCGGTGCTGTCGTCCAGTTGCACCATCCAGGCGTACATCACGTGGACCTTAATTACCGTGTGGCTG
CAGAGATGGGTGGAAGAGTCCACCCACCAAACCTCGAACGCCAAGAAGAAAAGGTCCCTGACTAAAGGCAGGTCTTCTAA
GAAAGGAGCAGAGAATGGTGTGGAATCCGCCAGCAGGGTAGACGCCCTTCCAAAGAGGAAAGAGAAATCTTCATGA

ORF - retro_ocun_52 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.25 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAIRKKSTKSPPVLSHEFILQNHADIVSCVAMVFLLGLMFEITAKASIIFVTLQYNVTVPATEEQAAESA
M..RKKS.K.PP.LS.EFILQNHADI.SCV.M.FLLGLMFE.TA..SI.F.TLQ..VTVPATEEQA..S.
RetrocopyMGFRKKSSKNPPMLSQEFILQNHADIASCVGMFFLLGLMFEGTAGVSIVFLTLQHGVTVPATEEQASGSR
ParentalSLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
SLY.YG.KDLATVFFYMLVAIIIHA.IQEYVLDKIN.RM.F.K.K..KFNESGQ.S.FY...C.WGT.IL
RetrocopySLYHYGGKDLATVFFYMLVAIIIHATIQEYVLDKINKRMQFTKAKQNKFNESGQFSVFYFVSCIWGTIIL
ParentalISENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWFHAFPELYFQKTKKEDVPRQLVYIGLYLFHIAGA
ISEN...DPT.LWR..P.N.MTFQMKFFYISQLAYWFH.FPELYFQK..K.D.PRQL.YIGL.LFHI.GA
RetrocopyISENCLADPTLLWRSHPPNMMTFQMKFFYISQLAYWFHGFPELYFQKIRKQDIPRQLIYIGLHLFHISGA
ParentalYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
YLL.LNHLGL.LLVLHYFVE.L.H...LFYFSDEKYQKG.SLWA..F.LGRL.TLI.SVLTVGF.LA...
RetrocopyYLLYLNHLGLLLLVLHYFVELLSHMCGLFYFSDEKYQKGLSLWALVFILGRLTTLIVSVLTVGFHLAGSQ
ParentalNQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSTFQAPVVKKKPTVTKGRSSRKGT
....D..TGN.NVLA..IAVL.S.C..QA...W..I...L.RW.E.ST.Q....KKK...TKGRSS.KG.
RetrocopyTRDPDALTGNVNVLAAKIAVLSSSCTIQAYITWTLITVWLQRWVEESTHQTSNAKKKRSLTKGRSSKKGA
ParentalENGVNGTVTSNGADSPRNRKEKSS
ENGV.........D....RKEKSS
RetrocopyENGVE---SASRVDALPKRKEKSS

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 6 .46 RPM 32 .95 RPM
SRP017611_kidney 0 .00 RPM 138 .76 RPM
SRP017611_liver 0 .00 RPM 137 .89 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_52 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_52 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_52 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_117
Parental genes homology:
Parental genes homology involve 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG00000008734 1 retrocopy
retro_ocun_52 ,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,


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