RetrogeneDB ID:

retro_btau_24

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:6:9455205..9456342(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000046440
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TRAM1
Ensembl ID:ENSBTAG00000007562
Aliases:TRAM1, TRAM
Description:translocating chain-associated membrane protein 1 [Source:RefSeq peptide;Acc:NP_001035566]


Retrocopy-Parental alignment summary:






>retro_btau_24
ATGACGTTTCGTAAGAAGGGCTCCAAGAACCCCCCACTCCTGAGCCTGGAATTCATCCTGCAGAATCATGCGGACTTTGT
CGCCTGTGTGGGGATGTTCTTCGTGCTGGGGCTCATGTTCGAGGGGACAGCAGAAGTGTCGATCGTTTTTATTACTCTCC
AGCACGGGGTTACCTTCCCTGCAGCAGAAGCAGAAGCAGAAGCAGAAGCAGAACGAGCCACAGCACCCAAGTTCCTTTAT
CATTATGGTGCCAAAGACTTGGCCACGGTGTTCTTCTATACGCTGGTGGCAATCATCATTCACGCCACCATTCAGGAGTA
CGTGTTGGATAGAATTAACAGGCGAATGCAGTTCCCCAAACAGAGGCAAGGCAAATTTTATGAATCTGGTCAGTTTAGCG
TATTCTTCCTTGTCTCCTGTATCTGGGGCACATTCATTCTAGTTTCTGAAAACTGCCTGTCAGACCTGGCTGTCTTATGG
AAGGCTCATACCCATAACATGATGACATTTCAGATGAAGTTTTTCTACATCTCCCAGTTGGCTTACTGGTTTCACGCCTT
TCCCGAACTACTATTCCAGAGAAGCAGACCTCAAGAACTCTCCCAGCAAGCTGTATATGTTGGTCTTCACCTCTTTCACA
TTGCGGGAGCTTATCTCTTGTACTTGAATCACCTGGGACTTCTTCTTTTGATGATGCATTATTTTGTGGAATTCCTTTCC
CACTCTTGCGACCTGTTTTATTTTAGCGACGAGAAGTTCCAGAAGGAGTTTTCTCTATGGGCCATTGTGTTTATTTTGGG
TCGACTTGTGACTTTAATTGTTTCTTTGATAACTGCTGGTTTTCAGCTGGCTGGAGGGCATAATGTGATTTCGGATGACT
CTGCTGAAGACGTGAACGTGTTGGCAGCTAAAATCGCTGTTCTGTCATCCAGTTGCTCTATCCAAGCATACGTAACATGG
AATTTATTTAATGTTCAGCTTCAGAGGTGGATGGAAGAAGATGCGCCTCTTCAGGCCCCAAGTGTGAAGAAGAAACGGAT
TAAGGGCAGATTTTGTAGAAAAGGAACGGAAAACGGTGTGGCAACTTCAAATAGACTACTAGATTCTCCCCAGATGAGGA
AAGAAAAGTCTTCATAA

ORF - retro_btau_24 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.76 %
Parental protein coverage: 83.96 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalATEEQATESAFLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYL
A..E.AT...FLY.YG.KDLATVFFY.LVAIIIHA.IQEYVLD.INRRM.F.K....KF.ESGQ.S.F.L
RetrocopyAEAERATAPKFLYHYGAKDLATVFFYTLVAIIIHATIQEYVLDRINRRMQFPKQRQGKFYESGQFSVFFL
ParentalFSCIWGTFILVSENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWFHAFPELYFQKTKKEDIPRQLVYI
.SCIWGTFILVSEN..SD...LW.A..HN.MTFQMKFFYISQLAYWFHAFPEL.FQ.........Q.VY.
RetrocopyVSCIWGTFILVSENCLSDLAVLWKAHTHNMMTFQMKFFYISQLAYWFHAFPELLFQRSRPQELSQQAVYV
ParentalGLYLFHIAGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVL
GL.LFHIAGAYLL.LNHLGL.LL..HYFVEFL.H...LFYFSDEK.QK.FSLWA..F.LGRL.TLI.S..
RetrocopyGLHLFHIAGAYLLYLNHLGLLLLMMHYFVEFLSHSCDLFYFSDEKFQKEFSLWAIVFILGRLVTLIVSLI
ParentalTVGFGLARAENQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSA-FQAPAVKKKPP
T.GF.LA...N...D.S....NVLA..IAVL.S.C..QA...W...N.QL.RW.E..A..QAP.VKKK..
RetrocopyTAGFQLAGGHNVISDDSAEDVNVLAAKIAVLSSSCSIQAYVTWNLFNVQLQRWMEEDAPLQAPSVKKKR-
ParentalVTKGRSSRKGTENGVNGTVTSNGADSPRNRKEKSS
..KGR..RKGTENGV.........DSP..RKEKSS
Retrocopy-IKGRFCRKGTENGV--ATSNRLLDSPQMRKEKSS

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 0 .00 RPM 78 .95 RPM
ERP005899_muscle 0 .05 RPM 100 .46 RPM
SRP017611_brain 3 .84 RPM 14 .11 RPM
SRP017611_kidney 0 .12 RPM 99 .69 RPM
SRP017611_liver 0 .00 RPM 289 .88 RPM
SRP030211_testis 0 .41 RPM 198 .85 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_24 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_24 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_24 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Sus scrofa retro_sscr_980
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 ENSBTAG00000007562 1 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 ENSOCUG000000087341 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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