RetrogeneDB ID: | retro_btau_1026 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 23:29411621..29412041(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000027279 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM177A1 | ||
| Ensembl ID: | ENSBTAG00000009680 | ||
| Aliases: | None | ||
| Description: | Protein FAM177A1 [Source:UniProtKB/Swiss-Prot;Acc:A6QLZ5] |
Retrocopy-Parental alignment summary:
>retro_btau_1026
ATGGAGCGGGAGCCAGCGAGCTGTGAGGAGGGAGAAGCCGTGAATGCCTCGGGAGCTGCGGCCGCCTCGGCGTTCAGGGA
ATCGGCACAGCAGATGAGTAATGAAAGAGGCTTTGAAAATGTAGAACTGGGAGTCATAGGAAAAAAGAAGAAAGTCCCAA
GGAGAGTCATCCACTTTGTTAGCGGTGAAACAATGGAAGAGTACAGCACAGACGAAGATGAAGTGGACAGCCTGGAGAAG
AAAGACGTTCTGCCTCCTGTTGATCCGACAAAACTTACCTGGGGCCCCTACTTATGGTTTCACATGCTTCGTGCTGCCAC
ATCCACCCTCTCAGTTTGTGACTTTCTTGGAGAGAAGATTGCATCTGTTTTGGGCATCAGCACCCCAAAATACCAGTATG
CAATTGATGAGTATTACCGG
ORF - retro_btau_1026 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.57 % |
| Parental protein coverage: | 66.04 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEGEPASREEGEAVNASGAAAASAFRESAQQMSNERGFENVELGVIGKKKKVPRRVIHFVSGETMEEYST |
| ME.EPAS.EEGEAVNASGAAAASAFRESAQQMSNERGFENVELGVIGKKKKVPRRVIHFVSGETMEEYST | |
| Retrocopy | MEREPASCEEGEAVNASGAAAASAFRESAQQMSNERGFENVELGVIGKKKKVPRRVIHFVSGETMEEYST |
| Parental | DEDEVDSLEKKDVLPPVDPTKLTWGPYLWFHMLRAATSTLSVCDFLGEKIASVLGISTPKYQYAIDEYYR |
| DEDEVDSLEKKDVLPPVDPTKLTWGPYLWFHMLRAATSTLSVCDFLGEKIASVLGISTPKYQYAIDEYYR | |
| Retrocopy | DEDEVDSLEKKDVLPPVDPTKLTWGPYLWFHMLRAATSTLSVCDFLGEKIASVLGISTPKYQYAIDEYYR |
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 .07 RPM | 12 .76 RPM |
| ERP005899_muscle | 0 .11 RPM | 19 .64 RPM |
| SRP017611_brain | 0 .05 RPM | 35 .13 RPM |
| SRP017611_kidney | 0 .06 RPM | 25 .90 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .87 RPM |
| SRP030211_testis | 3 .32 RPM | 46 .88 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1026 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1026 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1026 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009680 | 1 retrocopy |
retro_btau_1026 ,
|
| Sorex araneus | ENSSARG00000004821 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000009637 | 1 retrocopy |