RetrogeneDB ID: | retro_btau_92 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 10:42699098..42699419(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000025564 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RPL36A | ||
| Ensembl ID: | ENSBTAG00000019253 | ||
| Aliases: | None | ||
| Description: | 60S ribosomal protein L36a [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ59] |
Retrocopy-Parental alignment summary:
>retro_btau_92
ATGGTCAACGTACCTAAAACCCGCAGGACTTTCTGTAAGAAGTGTGGAAAGCATCAGCCTCACAAAGTGACCCAGTATAA
GAAGGGCAAAGATTCCCTGTATGCCCAGGGAAAGAGGCGCTATGATCGGAAGCAAAGTGGCTACGGTGGGCAAACCAAGC
CAATTTTCCGGAAGAAGGCTAAAACCACCAAGAAGATCGTGCTGAGACTTGAATGCGTTGAGCCCAACTGCAGATCCAAG
AGGATGCTGGCCATTAAGAGGTGCAAGCATTTTGAACTTGGAGGAGATAAGAAGAGAAAGGGCCAAGTGATCCAGTTCTA
A
ORF - retro_btau_92 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL |
| MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL | |
| Retrocopy | MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL |
| Parental | ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF |
| ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF | |
| Retrocopy | ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF |
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 | 37 .92 RPM | 63 .88 RPM |
| ERP005899_muscle | 145 .75 RPM | 213 .64 RPM |
| SRP017611_brain | 24 .44 RPM | 20 .51 RPM |
| SRP017611_kidney | 63 .36 RPM | 45 .22 RPM |
| SRP017611_liver | 52 .18 RPM | 21 .82 RPM |
| SRP030211_testis | 33 .80 RPM | 16 .26 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_92 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_92 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_92 has 6 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2 |
| Gorilla gorilla | retro_ggor_208 |
| Pongo abelii | retro_pabe_55 |
| Callithrix jacchus | retro_cjac_55 |
| Mus musculus | retro_mmus_4 |
| Equus caballus | retro_ecab_204 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000008503 | 1 retrocopy | |
| Bos taurus | ENSBTAG00000019253 | 3 retrocopies |
retro_btau_183, retro_btau_241, retro_btau_92 ,
|
| Loxodonta africana | ENSLAFG00000017385 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000025578 | 2 retrocopies | |
| Sarcophilus harrisii | ENSSHAG00000013479 | 1 retrocopy |