RetrogeneDB ID:

retro_btau_268

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:1:91626083..91626864(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.65952
Ensembl ID:ENSBTAG00000017225
Aliases:None
Description:E3 ubiquitin-protein ligase RNF135 [Source:RefSeq peptide;Acc:NP_001092406]


Retrocopy-Parental alignment summary:






>retro_btau_268
TTGTCGGATGGTGTGAACTTTCCTTGGCTTCTCCCAAACTAGTGACTTCATGCCCACCTGAGCAAAAAAATGAAAGATAT
TCTCTATGACCTAGAAGAGATCCAGGGAAAATTACAAGAAAATTTCACTCAGCAATGGGCCCTTGAAGAACGAACACAGG
TTGAACTCCCGGAAGCTCCATCTTCTTCCTCATGCTCACTGCCTGACCAGAGCCACCTTGCACCCAAGAGGTTTCTTCAT
CTGCTCGATAGACCATCATCAGTCCAAACTTTGACCTTGGGAGCCTCTCCTATAATCTGAAGGTGTCCACAGATCACTGG
ACAGTGACTGTATCTCACTTTCCACACACCTGACCCTGGAGTCCTGAAAGGTTTGCCTCCAGCCAAGCCATATGTTTCCA
GGCCCTCTCTTCTGGGCAGCAGTATTGGGAAGTGGACACTCAGCATTGTAGCCACTGGACAGTTGGGGTGACCTTGTGGA
GGGATGAAGAAAAGCCAGATCCTAGGAAGGACCACAGACTCCTGGTGTATAGAGTGGGAAAGGGACCAGCCAGCTGTCTG
CATGGTGCACAGTCAAGGAAACTGTCTTCGACTCACACAGACCTAGTGTGGTGGACATCTGGCTAGACCTTGAGGAGGGA
AATCTTGCCTTTTATTCTGTGGCTGATCTGGCGAAGCCTCTGTATGAGTGCCCAGTCTCTGTCTCTTTTCCTCTGCACCT
TGCCTTCTGCCTGTATGACTTATACCCTGGAAATTCTCTGACTATAAGGCAAAAGAACATG

ORF - retro_btau_268 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.72 %
Parental protein coverage: 60.85 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLLDGV-DLSLASPK-VSSSPPEQK-MKDILHDLEEIQEKLRENFTQKGALEEQTQVELPEVPSSSSCPLP
L.DGV..LSLASPK.V.S.PPEQK.MKDIL.DLEEIQ.KL.ENFTQ..ALEE.TQVELPE.PSSSSC.LP
RetrocopyLSDGV<ELSLASPKLVTSCPPEQK>MKDILYDLEEIQGKLQENFTQQWALEERTQVELPEAPSSSSCSLP
ParentalDQSRFAPKK-ASSFAR-WAISPTFDLESLSCNLKVSVDLRTVTVSDFPMLYAWSPERFASSQALCSQALS
DQS..APK...SS.AR...ISP.FDL.SLS.NLKVS.D..TVTVS.FP....WSPERFASSQA.C.QALS
RetrocopyDQSHLAPKR<VSSSAR*TIISPNFDLGSLSYNLKVSTDHWTVTVSHFPHT*PWSPERFASSQAICFQALS
ParentalSGQHYWEVDTQRCSHWAVGVA-SRGMKRDQILGRTTDSWCVEW-KGASQLSAWCMVKETVLGSDRPSVVG
SGQ.YWEVDTQ.CSHW.VGV....GMK..QILGRTTDSWC.EW.KG.SQLSAWC.VKETV..S.RPSVV.
RetrocopySGQQYWEVDTQHCSHWTVGVT>CGGMKKSQILGRTTDSWCIEW>KGTSQLSAWCTVKETVFDSHRPSVVD
ParentalIWLDLEEGKLAFYSKADQAKPLFECPISVSVPLHPAFWLYGLDPGNSLTIRKMNV
IWLDLEEG.LAFYS.AD.AKPL.ECP.SVS.PLH.AF.LY.L.PGNSLTIR..N.
RetrocopyIWLDLEEGNLAFYSVADLAKPLYECPVSVSFPLHLAFCLYDLYPGNSLTIRQKNM

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 25 .59 RPM
ERP005899_muscle 0 .00 RPM 36 .90 RPM
SRP017611_brain 0 .00 RPM 15 .35 RPM
SRP017611_kidney 0 .00 RPM 52 .57 RPM
SRP017611_liver 0 .00 RPM 23 .11 RPM
SRP030211_testis 0 .00 RPM 9 .97 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_268 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_268 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_268 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000017225 1 retrocopy
retro_btau_268 ,


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