RetrogeneDB ID: | retro_btau_1571 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 7:39875978..39876428(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000010020 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HMG20B | ||
| Ensembl ID: | ENSBTAG00000047668 | ||
| Aliases: | None | ||
| Description: | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related [Source:UniProtKB/Swiss-Prot;Acc:Q32L68] |
Retrocopy-Parental alignment summary:
>retro_btau_1571
ATGTCCCACGGCCCCAAGCAGCCCGGCGCGGCCTCCGCGCCCGCGAGCGGCAAGGCTCCAGGACAGCATGGGGGCTTCGT
GGTGGCTGTCAAGCAAGAGCGCGGCGAGGGCCCGCGGGCCGGAGAGAAGGGGTCCCACGAAGAGGAGCCGATGAAGAAGC
GCGGCTGGCCCAAGGGCAAGAAGCGGAAGAAGATCCTGCCGAATGGGCCCAAGGCACCTGTCACCGGCTACGTGCGTTTC
CTGAACGAGCGGCGCGAGCAGATCCGGACGCGCCACCCGGACCTGCCCTTTCCCGAGATCACCAAGATGCTGGGCGCCGA
GTGGAGCAAGCTGCAGCCGGCGGAGAAACAGCGGTACTTGGACGAGGCTGAACGGGAGAAGCAGCAGTACATGAAGGAGC
TGAGGGCCTACCAGCAGTCGGAAGCCTACAAGATGTGTGCGGAGAAGATC
ORF - retro_btau_1571 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.67 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSHGPKQPGAASAPASGKAPGQHGSFVVAVKQERGEGPRAGEKGSHEEEPVKKRGWPKGKKRKKILPNGP |
| MSHGPKQPGAASAPASGKAPGQHG.FVVAVKQERGEGPRAGEKGSHEEEP.KKRGWPKGKKRKKILPNGP | |
| Retrocopy | MSHGPKQPGAASAPASGKAPGQHGGFVVAVKQERGEGPRAGEKGSHEEEPMKKRGWPKGKKRKKILPNGP |
| Parental | KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQS |
| KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQS | |
| Retrocopy | KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQS |
| Parental | EAYKMCAEKI |
| EAYKMCAEKI | |
| Retrocopy | EAYKMCAEKI |
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 .94 RPM | 0 .36 RPM |
| ERP005899_muscle | 3 .64 RPM | 9 .40 RPM |
| SRP017611_brain | 1 .92 RPM | 3 .24 RPM |
| SRP017611_kidney | 6 .16 RPM | 7 .41 RPM |
| SRP017611_liver | 2 .57 RPM | 6 .19 RPM |
| SRP030211_testis | 17 .80 RPM | 47 .87 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1571 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1571 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1571 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 | ENSBTAG00000047668 | 1 retrocopy |
retro_btau_1571 ,
|
| Myotis lucifugus | ENSMLUG00000022392 | 1 retrocopy |