RetrogeneDB ID: | retro_btau_131 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 14:58850397..58850958(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000006213 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IFT27 | ||
| Ensembl ID: | ENSBTAG00000026657 | ||
| Aliases: | IFT27, RABL4 | ||
| Description: | Intraflagellar transport protein 27 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q0VCN3] |
Retrocopy-Parental alignment summary:
>retro_btau_131
ATGGTGAAGCTCGCAGCCAAATGCATCCTGGCAGGAGACCCCACCGTGGGCAAGACCGCCCTGGCACAGCTCTTCCACAG
CGACGGGGCCCATTTCCAGAAGAACTACACCCTGACAACAGGGGTGGATCTGGTGGTGAAAACAGTGGCAGTCCCTGACA
CGGGGGACAGTGTGGAACTCTTCATTTTTGACTCGGCCGGCAAAGAGCTGTTTTCTGAAATGCTGGATAAACTGTGGGAG
AGTCCCAATGTCTTGTGTCTTGTCTACGACGTGACCAACGAGCAGTCCTTCACCAACTGCAGCAAGTGGCTGGAGAAGGC
TCGGTCTCAGATTCCAGGGACCACCCTCCCAGGTGTGCTAGTGGGAAACAAGACAGACCTGGCTGGCAGGCGAGTGGTGG
ATGTGGCCCAGGCCCAGGCGTGGGCACTGGGCCAAGGCCTGGAATGTTTTGAAACATCCGTGAAGGAGATGGAAAACTAT
GAAGCCCCTTTCCACTACCTGGCCAAGCAGTTTCACCACCTGTACCGGGAGAAGCTGGAGGTTTTCCAGGTGCTGGTGTG
A
ORF - retro_btau_131 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.39 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVKLAAKCILAGDPTVGKTALAQLFRSDGAHFQKNYTLTTGVDLVVKTVPVPDTGDSVELFIFDSAGKEL |
| MVKLAAKCILAGDPTVGKTALAQLF.SDGAHFQKNYTLTTGVDLVVKTV.VPDTGDSVELFIFDSAGKEL | |
| Retrocopy | MVKLAAKCILAGDPTVGKTALAQLFHSDGAHFQKNYTLTTGVDLVVKTVAVPDTGDSVELFIFDSAGKEL |
| Parental | FSEMLDKLWESPNVLCLVYDVTNEQSFTNCSKWLEKARSQIPGTTLPGVLVGNKTDLAGRRVVDVAQAQA |
| FSEMLDKLWESPNVLCLVYDVTNEQSFTNCSKWLEKARSQIPGTTLPGVLVGNKTDLAGRRVVDVAQAQA | |
| Retrocopy | FSEMLDKLWESPNVLCLVYDVTNEQSFTNCSKWLEKARSQIPGTTLPGVLVGNKTDLAGRRVVDVAQAQA |
| Parental | WALGQGLECFETSVKEMENYEAPFHYLAKQFHHLYREKLEVFQALV |
| WALGQGLECFETSVKEMENYEAPFHYLAKQFHHLYREKLEVFQ.LV | |
| Retrocopy | WALGQGLECFETSVKEMENYEAPFHYLAKQFHHLYREKLEVFQVLV |
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 | 0 .65 RPM |
| ERP005899_muscle | 0 .00 RPM | 3 .11 RPM |
| SRP017611_brain | 0 .27 RPM | 8 .41 RPM |
| SRP017611_kidney | 0 .36 RPM | 5 .93 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .06 RPM |
| SRP030211_testis | 3 .12 RPM | 57 .86 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_131 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_131 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_131 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 | ENSBTAG00000026657 | 1 retrocopy |
retro_btau_131 ,
|
| Callithrix jacchus | ENSCJAG00000013961 | 1 retrocopy |