RetrogeneDB ID: | retro_btau_675 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 17:37982386..37982938(-) | ||
| Located in intron of: | ENSBTAG00000047595 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.49010 | ||
| Ensembl ID: | ENSBTAG00000001212 | ||
| Aliases: | None | ||
| Description: | translocon-associated protein subunit beta precursor [Source:RefSeq peptide;Acc:NP_001015533] |
Retrocopy-Parental alignment summary:
>retro_btau_675
CTGAGGCTGCTGGAGTTTGTGGTGTTCATTCTATTTGCCGTCACACAAGCAGACAAAGTAGCCAGGCTTTGGCCTCAAAA
TCACTGTTGAACAGATGTGCTGTGAAAGGGGAGACCTGATCTTTCAGAACAATATCTACAGTATTGGCTCAAGTGCTACA
TGAGACGTGGACTTGCCTGATGATTCCTTCCTTCCAGAAGACTTCAGCATTGTCTTGGGAATAATCAACATTAAATGGGA
CTGGGTTACTCCTGCTAACAATGTCTCTCACATCATGGCCCTACATCCTCTCAAGGCTGGTTATTTCAGCTTCACCTCAG
CAACTATTCCTTACCTGGCTCAAGAGGATAGGCCCATAGTGATGGACTTTACCAGTGCACCTGAATGGGGAGGAATCCTG
GCTCAGCATAGTTGAATTGTAGATTTTTCCCCCATTTTTTCCTGGACTGCGTAGCTTTCCGGGTTATGACTCTCCCTTCA
ATGGACATCCACCTGCAGTCATGATACTCCAGCAAGAGGAAATATGACATCCCCCAAACCAAAAAAATAACT
ORF - retro_btau_675 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.83 % |
| Parental protein coverage: | 86.79 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MRLLAFAVLALFAVTQAEEGARL-LASKSLLNRYAVEGR-DLTLQYNIYNVGSSAALDVELSDDSFPPED |
| .RLL.F.V..LFAVTQA...ARL.LASKSLLNR.AV.G..DL..Q.NIY..GSSA..DV.L.DDSF.PED | |
| Retrocopy | LRLLEFVVFILFAVTQADKVARL<LASKSLLNRCAVKGE<DLIFQNNIYSIGSSAT*DVDLPDDSFLPED |
| Parental | FGIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATVTYLAQEDGPVVIGFTSAPGQGGILAQRE |
| F.IV.G..N.KWD...PA.NVSH...L.PLKAGYF.FTSAT..YLAQED.P.V..FTSAP..GGILAQ.. | |
| Retrocopy | FSIVLGIINIKWDWVTPANNVSHIMALHPLKAGYFSFTSATIPYLAQEDRPIVMDFTSAPEWGGILAQHS |
| Parental | -FDRRFSPH-FLDWAAFGVMTLPSIGVPLLLWYSSKRKYDTPKTKRLS |
| ....RF.PH.FLD..AF.VMTLPS....L...YSSKRKYD.P.TK... | |
| Retrocopy | <LNCRFFPHFFLDCVAFRVMTLPSMDIHLQS*YSSKRKYDIPQTKKIT |
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 | 85 .87 RPM |
| ERP005899_muscle | 0 .00 RPM | 336 .37 RPM |
| SRP017611_brain | 0 .00 RPM | 66 .28 RPM |
| SRP017611_kidney | 0 .00 RPM | 112 .44 RPM |
| SRP017611_liver | 0 .00 RPM | 219 .20 RPM |
| SRP030211_testis | 0 .06 RPM | 55 .10 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_675 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_675 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_675 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000001212 | 2 retrocopies |
retro_btau_1165, retro_btau_675 ,
|
| Cavia porcellus | ENSCPOG00000023729 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000012304 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000028971 | 1 retrocopy |