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:
| Parental | LLDGV-DLSLASPK-VSSSPPEQK-MKDILHDLEEIQEKLRENFTQKGALEEQTQVELPEVPSSSSCPLP |
| L.DGV..LSLASPK.V.S.PPEQK.MKDIL.DLEEIQ.KL.ENFTQ..ALEE.TQVELPE.PSSSSC.LP | |
| Retrocopy | LSDGV<ELSLASPKLVTSCPPEQK>MKDILYDLEEIQGKLQENFTQQWALEERTQVELPEAPSSSSCSLP |
| Parental | DQSRFAPKK-ASSFAR-WAISPTFDLESLSCNLKVSVDLRTVTVSDFPMLYAWSPERFASSQALCSQALS |
| DQS..APK...SS.AR...ISP.FDL.SLS.NLKVS.D..TVTVS.FP....WSPERFASSQA.C.QALS | |
| Retrocopy | DQSHLAPKR<VSSSAR*TIISPNFDLGSLSYNLKVSTDHWTVTVSHFPHT*PWSPERFASSQAICFQALS |
| Parental | SGQHYWEVDTQRCSHWAVGVA-SRGMKRDQILGRTTDSWCVEW-KGASQLSAWCMVKETVLGSDRPSVVG |
| SGQ.YWEVDTQ.CSHW.VGV....GMK..QILGRTTDSWC.EW.KG.SQLSAWC.VKETV..S.RPSVV. | |
| Retrocopy | SGQQYWEVDTQHCSHWTVGVT>CGGMKKSQILGRTTDSWCIEW>KGTSQLSAWCTVKETVFDSHRPSVVD |
| Parental | IWLDLEEGKLAFYSKADQAKPLFECPISVSVPLHPAFWLYGLDPGNSLTIRKMNV |
| IWLDLEEG.LAFYS.AD.AKPL.ECP.SVS.PLH.AF.LY.L.PGNSLTIR..N. | |
| Retrocopy | IWLDLEEGNLAFYSVADLAKPLYECPVSVSFPLHLAFCLYDLYPGNSLTIRQKNM |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_268 retrocopy.
Bos taurus was not studied using FANTOM5 data.
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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