RetrogeneDB ID: | retro_cpor_232 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_103:1646703..1646922(-) | ||
| Located in intron of: | ENSCPOG00000013291 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GABARAPL1 | ||
| Ensembl ID: | ENSCPOG00000006718 | ||
| Aliases: | None | ||
| Description: | Gamma-aminobutyric acid receptor-associated protein-like 1 [Source:UniProtKB/Swiss-Prot;Acc:P60518] |
Retrocopy-Parental alignment summary:
>retro_cpor_232
GTACCTGATCTGAACAAGGGGAAGTACCTAGTGCCTTCTGACATGGTTGGCCAGTTTTACTTCTTAATCTGGAAGAAACT
GATTAAGAACACCCAAAGACCCCTTATTCGCTGTCAACATCCCTCCCATTAGTGTTACTTGGGCCACCCATACGAGAACA
CCCCATGAGGAAGACTACTTTCTGTCTGTGGCCCAACAGGGATGAGAGTCTATGGGAAG
ORF - retro_cpor_232 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.43 % |
| Parental protein coverage: | 65.81 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VPDLDKRKYLVPSDLTVGQFYFLIRKRIHLR-PEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAY |
| VPDL.K.KYLVPSD..VGQFYFLI.K......P.D.LF......IPP.S.T........HEEDYFL.VA. | |
| Retrocopy | VPDLNKGKYLVPSDM-VGQFYFLIWKKLIKN>PKDPLFAV---NIPPISVTWATHTRTPHEEDYFLSVAQ |
| Parental | -SDESVYGK |
| .....VYGK | |
| Retrocopy | <TGMRVYGK |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 351 .66 RPM |
| SRP017611_kidney | 0 .00 RPM | 432 .78 RPM |
| SRP017611_liver | 0 .00 RPM | 313 .78 RPM |
| SRP040447_lung | 0 .00 RPM | 158 .87 RPM |
| SRP040447_skeletal_muscle | 0 .01 RPM | 32 .69 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_232 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_232 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 7 parental genes, and 27 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000006718 | 1 retrocopy |
retro_cpor_232 ,
|
| Cavia porcellus | ENSCPOG00000023922 | 1 retrocopy | |
| Homo sapiens | ENSG00000139112 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000016834 | 3 retrocopies | |
| Sarcophilus harrisii | ENSSHAG00000007434 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000002246 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000005307 | 19 retrocopies |
retro_tsyr_1045, retro_tsyr_1070, retro_tsyr_1101, retro_tsyr_1137, retro_tsyr_1308, retro_tsyr_1413, retro_tsyr_1467, retro_tsyr_1481, retro_tsyr_1671, retro_tsyr_1765, retro_tsyr_1800, retro_tsyr_234, retro_tsyr_573, retro_tsyr_761, retro_tsyr_796, retro_tsyr_832, retro_tsyr_864, retro_tsyr_978, retro_tsyr_999,
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