RetrogeneDB ID: | retro_mmul_301 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 5:91371904..91372636(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMMUG00000030225 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FGF13 | ||
| Ensembl ID: | ENSMMUG00000012484 | ||
| Aliases: | None | ||
| Description: | fibroblast growth factor 13 [Source:RefSeq peptide;Acc:NP_001252772] |
Retrocopy-Parental alignment summary:
>retro_mmul_301
ATGGCGGCGGCTATCGCCAGCTCGCTCATCCGTCAGAAGAGGCAAGGCCGCGAGCGCGAGAAATCCAACGCCTGCAAGTG
CAGTCCCAGCAAAGGCAAGACCAGCTGCGACAAAAACAAGTTAAATGTCTTTTCCCGGGTCAAACTCTTCGGCTCCAAGA
AGAGGCCCCGAAGAAGACCAGAGCCTCAGCTTAAGGGTGTAGTTACCAAGCTATACAGCCGACAAGGCTACCACTTGCAG
CTGCAGGCGGATGGAACCATTGATGGCACCAAAGATGAGGACAGCACTTACACTCTGTTTAACCTCATCCCTGTGGGTCT
GCGAGTGGTGGCTATGCAAGGAGTTCAAACCAAGCTGTACTTGGCAATGAACAGTGAGGGATCCTTGTACACTTCGGAAC
TTTTCACACCTGAGTGCAAATTCAAAGAATCAGTGTTTGAAAATTATTATGTGACATATTCATCAATGATATACCGTCAG
CAGCAGTCAGGCCGAGGGTGGTATCTGGGTCTGAACAAAGAAGGAGAGATCATGAAAGGCAACCATGTGAAGAAGAACAA
GCCTGCAGCTCATTTTCTGCCCAAACCACTAAAAGTGGCCATGTACAAGGAGCCATCACTGCACGACCTCACGGAGTTCT
CCCGATCTGGAAGCGGGACCCCAACCAAGAGCAGAAGTGTCTCTGGCGTGCTGAACGGAGGCAAATCCATGAGCCACAAT
GAATCAACGTAG
ORF - retro_mmul_301 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.14 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAAIASSLIRQKRQAREREKSNACKCVSSPSKGKTSCDKNKLNVFSRVKLFGSKKRRRRRPEPQLKGIV |
| MAAAIASSLIRQKRQ.REREKSNACKC..SPSKGKTSCDKNKLNVFSRVKLFGSKKR.RRRPEPQLKG.V | |
| Retrocopy | MAAAIASSLIRQKRQGREREKSNACKC--SPSKGKTSCDKNKLNVFSRVKLFGSKKRPRRRPEPQLKGVV |
| Parental | TKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQGVQTKLYLAMNSEGYLYTSELFTPE |
| TKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVA.QGVQTKLYLAMNSEG.LYTSELFTPE | |
| Retrocopy | TKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAMQGVQTKLYLAMNSEGSLYTSELFTPE |
| Parental | CKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLH |
| CKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLH | |
| Retrocopy | CKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLH |
| Parental | DLTEFSRSGSGTPTKSRSVSGVLNGGKSMSHNEST |
| DLTEFSRSGSGTPTKSRSVSGVLNGGKSMSHNEST | |
| Retrocopy | DLTEFSRSGSGTPTKSRSVSGVLNGGKSMSHNEST |
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 |
|---|---|---|
| SRP007412_brain | 0 .22 RPM | 34 .29 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .40 RPM | 31 .26 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 1 .74 RPM |
| SRP007412_heart | 0 .00 RPM | 2 .94 RPM |
| SRP007412_kidney | 0 .23 RPM | 2 .35 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .04 RPM |
| SRP007412_testis | 0 .04 RPM | 0 .64 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_301 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_301 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_301 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000004376 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000012484 | 1 retrocopy |
retro_mmul_301 ,
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