RetrogeneDB ID: | retro_btau_1712 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 9:85002558..85003296(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000037531 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FBXO25 | ||
| Ensembl ID: | ENSBTAG00000007039 | ||
| Aliases: | None | ||
| Description: | F-box only protein 25 [Source:UniProtKB/Swiss-Prot;Acc:Q1RMS8] |
Retrocopy-Parental alignment summary:
>retro_btau_1712
GAAAACTGGATCTATGTCCATAAAGAAAGCACAAGAGAAAGACATGGCTACTGTACTTTGGGAGAAGCTTTTAATCGCTT
AGACTTCTCGAGTGCGATCCAGGACATCCGAAGGTTCAATTATGTGGTCAGGCTATTGCAGCTGATTGCAAAGTCCCAGC
TGACCTCGCTGAGTGGTGTGGCCCAGAAGAACTACTTCAACATCCTGGATAAGATCGTTCAGAAGGTTCTCGGTGACCAC
CAAAACCCTCGCCTGATCAAGGATCTTCTCCAAGACCTCAGCTCCACCCTGTGCATTCTGATCCGAGGAGTAGGGAAGTC
TGTGCTGGTGGGAAACATCAACATCTGGATTTGCCGATTAGAGACCGTTCTCCGCTGGCAGCAGCAGCTGCAGAATCTTC
AGATGACGGAGGTGGACAGTGGCCTGACGCTCAGCGACCTTCCTGTGCACATGCTCAGCAACATCCTGTACAGGTTCTCG
GATGGGTGGGACATCGTCACCCTGGGTCAGGTGACCCCGACACTGTCCGCGCTCAGCGAGGACCGGCAGCTGTGGAAGAA
GCTCTGCCAGTACCACTTTGGGGAGAAGCAGTTTTGTAGACACTTGATCCTTTCAGAAAAAGGCCATGTGGAGTGGAAGC
TGATGTATTTTGCACTTCAGAAGCACTACCCCACCAAGGAGCAGTATGGAGACACCCTGCACTTCTGCCGGCACTGCAGC
ATCCTCTTCTGGAAGGAC
ORF - retro_btau_1712 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 68.91 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ENWIYVHKESTRERHGYCTLGEAFNRLDFSSAIQDIRRFNYVVRLLQLIAKSQLTSLSGVAQKNYFNILD |
| ENWIYVHKESTRERHGYCTLGEAFNRLDFSSAIQDIRRFNYVVRLLQLIAKSQLTSLSGVAQKNYFNILD | |
| Retrocopy | ENWIYVHKESTRERHGYCTLGEAFNRLDFSSAIQDIRRFNYVVRLLQLIAKSQLTSLSGVAQKNYFNILD |
| Parental | KIVQKVLGDHQNPRLIKDLLQDLSSTLCILIRGVGKSVLVGNINIWICRLETVLRWQQQLQNLQMTEVDS |
| KIVQKVLGDHQNPRLIKDLLQDLSSTLCILIRGVGKSVLVGNINIWICRLETVLRWQQQLQNLQMTEVDS | |
| Retrocopy | KIVQKVLGDHQNPRLIKDLLQDLSSTLCILIRGVGKSVLVGNINIWICRLETVLRWQQQLQNLQMTEVDS |
| Parental | GLTLSDLPVHMLSNILYRFSDGWDIVTLGQVTPTLSALSEDRQLWKKLCQYHFGEKQFCRHLILSEKGHV |
| GLTLSDLPVHMLSNILYRFSDGWDIVTLGQVTPTLSALSEDRQLWKKLCQYHFGEKQFCRHLILSEKGHV | |
| Retrocopy | GLTLSDLPVHMLSNILYRFSDGWDIVTLGQVTPTLSALSEDRQLWKKLCQYHFGEKQFCRHLILSEKGHV |
| Parental | EWKLMYFALQKHYPTKEQYGDTLHFCRHCSILFWKD |
| EWKLMYFALQKHYPTKEQYGDTLHFCRHCSILFWKD | |
| Retrocopy | EWKLMYFALQKHYPTKEQYGDTLHFCRHCSILFWKD |
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 | 15 .00 RPM |
| ERP005899_muscle | 0 .11 RPM | 17 .31 RPM |
| SRP017611_brain | 0 .96 RPM | 24 .03 RPM |
| SRP017611_kidney | 0 .18 RPM | 21 .93 RPM |
| SRP017611_liver | 0 .08 RPM | 6 .19 RPM |
| SRP030211_testis | 0 .78 RPM | 14 .80 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1712 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1712 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1712 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000007039 | 1 retrocopy |
retro_btau_1712 ,
|
| Cavia porcellus | ENSCPOG00000008110 | 1 retrocopy |