RetrogeneDB ID: | retro_btau_1488 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 6:28373361..28373874(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.70677 | ||
| Ensembl ID: | ENSBTAG00000014156 | ||
| Aliases: | None | ||
| Description: | protein AMN1 homolog [Source:RefSeq peptide;Acc:NP_001069326] |
Retrocopy-Parental alignment summary:
>retro_btau_1488
ATGCCCAGCCCTCAGCGGGTCAGTCAGCTCCCGGATCTATGCCTTTGGTGCTTCATGAAGGATATTTCTAGATATATCAC
AGACATTAAGCCTTTGCCACCCAACATAAAAGATAGACTCATCAAAATTATGAGCGTGCAGGGGCAGATAACAGATTCAA
ACATAAGTGAGATTTTACATCCTTTAGTCCAAACTCTAGATCTACGAAGCTGTGATATTTCAGATACTGCTCTCCTGCAC
CTGTGTAACTGTAGAAAACTGAAGAAATTAAATTGAAATTCCTCAAAAGAAAACAGAATTTCCATAACTTCAAAAGGAAT
AAAAGCTGTGGCTTCATCTTGTTCTTACCTGCATGAAGCTTCTTTGAAAAGATGCTGCAATCTCACTGATGAAGGAGTCC
TTGCTCTTGCACTCAATTGCCGGCTGTTAAAGATCATTGACTTAGGAGGCTGCTTAGGTATTACTGATGTGTTCTTGCAG
GCATTAGGAGAAAACTGTGCATTTTTGCAGTGT
ORF - retro_btau_1488 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.08 % |
| Parental protein coverage: | 66.28 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPSPQRVSQLLDLCLWCFMKNISRYITDIKPLPPNIKDRLIKIMSVQGQITDSNISEILHPEVQTLDLRS |
| MPSPQRVSQL.DLCLWCFMK.ISRYITDIKPLPPNIKDRLIKIMSVQGQITDSNISEILHP.VQTLDLRS | |
| Retrocopy | MPSPQRVSQLPDLCLWCFMKDISRYITDIKPLPPNIKDRLIKIMSVQGQITDSNISEILHPLVQTLDLRS |
| Parental | CDISDTALLHLCNCRKLKKLNLNSSKENRISITSKGIKAVASSCSYLHEASLKRCCNLTDEGVLALALNC |
| CDISDTALLHLCNCRKLKKLN.NSSKENRISITSKGIKAVASSCSYLHEASLKRCCNLTDEGVLALALNC | |
| Retrocopy | CDISDTALLHLCNCRKLKKLN*NSSKENRISITSKGIKAVASSCSYLHEASLKRCCNLTDEGVLALALNC |
| Parental | RLLKIIDLGGCLGITDVSLQALGENCAFLQC |
| RLLKIIDLGGCLGITDV.LQALGENCAFLQC | |
| Retrocopy | RLLKIIDLGGCLGITDVFLQALGENCAFLQC |
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 | 8 .87 RPM |
| ERP005899_muscle | 0 .00 RPM | 3 .06 RPM |
| SRP017611_brain | 0 .00 RPM | 18 .36 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .42 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .83 RPM |
| SRP030211_testis | 0 .15 RPM | 141 .39 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1488 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1488 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1488 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000014156 | 1 retrocopy |
retro_btau_1488 ,
|
| Canis familiaris | ENSCAFG00000010668 | 1 retrocopy | |
| Choloepus hoffmanni | ENSCHOG00000008485 | 2 retrocopies |