RetrogeneDB ID: | retro_btau_62 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 3:77154430..77154946(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000030890 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TTC9C | ||
| Ensembl ID: | ENSBTAG00000000773 | ||
| Aliases: | None | ||
| Description: | Tetratricopeptide repeat protein 9C [Source:UniProtKB/Swiss-Prot;Acc:A4IFF3] |
Retrocopy-Parental alignment summary:
>retro_btau_62
ATGGAGAAACGCCTGCAGGAGGCTCAGCTGTACAAGGAGAAAGGGAACCAGTGTTACCGGGAAGGGAAGTACCGGGATGC
TGTAAGTGGGTACCATCGAGCTCTGCTGCAGCTGCGGGGTCTGGATCCAAGTCTGCCCTCCCCGATACCTAATCTGGGAC
CTCAGGGCCTGGCCCTCACACCTGAACAAGAAAACCTACTTCACACCACCCAGACAGATTGCTACAACAACCTGGCTGCC
TGTCTCCTTCAGATGGAACCAGTAAACTATGAACGGGTGAAAGAGTACAGCCAGAAAGACGTGGAGCGGCAGCCTGATAA
TGCCAAGGCCTTGTATCGGGCTGGAGTGGCCTTTTTCCACCTGCAGGACTATGACCAGGCCCGGCACTACCTCATGGCTG
CTGTCAATAGGAAGCCAAAAGACGCCAATGTCCGGAGGTACCTTCAGCGGACACAGTTGGAACTCAGCAGCTACCATCGG
AAAGAGAAGCAGCTCTACCTGGGCATGTTTGGTTAA
ORF - retro_btau_62 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.25 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEKRLQEAQLYKEKGNQCYREGKYRDAVSGYHRALLQLRGLDPSLPSPIPNLGPQGPALTPEQENLLHTT |
| MEKRLQEAQLYKEKGNQCYREGKYRDAVSGYHRALLQLRGLDPSLPSPIPNLGPQG.ALTPEQENLLHTT | |
| Retrocopy | MEKRLQEAQLYKEKGNQCYREGKYRDAVSGYHRALLQLRGLDPSLPSPIPNLGPQGLALTPEQENLLHTT |
| Parental | QTDCYNNLAACLLQMEPVNYERVKEYSQKVLERQPDNAKALYRAGVAFFHLQDYDQARHYLMAAVNRKPK |
| QTDCYNNLAACLLQMEPVNYERVKEYSQK..ERQPDNAKALYRAGVAFFHLQDYDQARHYLMAAVNRKPK | |
| Retrocopy | QTDCYNNLAACLLQMEPVNYERVKEYSQKDVERQPDNAKALYRAGVAFFHLQDYDQARHYLMAAVNRKPK |
| Parental | DANVRRYLQRTQLELSSYHRKEKQLYLGMFG |
| DANVRRYLQRTQLELSSYHRKEKQLYLGMFG | |
| Retrocopy | DANVRRYLQRTQLELSSYHRKEKQLYLGMFG |
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 | 9 .52 RPM |
| ERP005899_muscle | 0 .16 RPM | 18 .21 RPM |
| SRP017611_brain | 0 .14 RPM | 7 .40 RPM |
| SRP017611_kidney | 0 .24 RPM | 11 .08 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .15 RPM |
| SRP030211_testis | 0 .36 RPM | 12 .19 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_62 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_62 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_62 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000773 | 2 retrocopies |
retro_btau_62 , retro_btau_78,
|