RetrogeneDB ID: | retro_itri_186 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | AGTP01152443.1:312..747(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSTOG00000025976 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_itri_186
GCCAGCACCCAAGCCAAGAGGATGGCCACGGTGTAAGTGTGCGGCGTCCAGGACTTGCTGTTTACCAGCAGCCCCTTCAT
GTGGAACCTGACAATGTACATGCTCTGGAGATGGTCTACAGAGTGGCTACTGGCTTGCCATCAGATGCTGCGGACATGTG
CAGGCTGCAGATGTGTACCTGATGACAGAGGACAGGCACTGCCAGGTACACCTTCTGGATGACAGAAGGCTGGAGCTGCT
GGTTCAGCCCAAACTTCTTTCAAGAGAGATGCTGCATCTGGTGGCTTCACAATTCAACCTGAAACAAAAGAGTACTTTTT
GTTCATAGATGACACTGGTCAGCAAAACTGGCTGCAGTTGGACCACTGAGTTATGGACCATGACCTGCCCAAGAAGACGG
GCCCAGCCGCCTTGCACCTTGCCATCAGGTTCCAC
ORF - retro_itri_186 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.52 % |
| Parental protein coverage: | 55.02 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | APARARRMASVFTCGVEDLLFAGSRFVWNLTVTTLRRWSSERLRACHQVLRT-WCGLR-DVYQMTEGRHC |
| A...A.RMA.V..CGV.DLLF..S.F.WNLT...L.RWS.E.L.ACHQ.LRT..C.L..DVY.MTE.RHC | |
| Retrocopy | ASTQAKRMATV*VCGVQDLLFTSSPFMWNLTMYMLWRWSTEWLLACHQMLRT<MCRLQ<DVYLMTEDRHC |
| Parental | QVHLLDDRRLELLVQPKLLSRELLDLVASHFNLKE-KEYFGITFTDDTGQQNWLQLDHRVLDHDLPKKPG |
| QVHLLDDRRLELLVQPKLLSRE.L.LVAS.FNLK..KEYF...F.DDTGQQNWLQLDH.V.DHDLPKK.G | |
| Retrocopy | QVHLLDDRRLELLVQPKLLSREMLHLVASQFNLKQ<KEYF--LFIDDTGQQNWLQLDH*VMDHDLPKKTG |
| Parental | PAALQFAVRFY |
| PAAL..A.RF. | |
| Retrocopy | PAALHLAIRFH |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_186 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_186 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus 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 1 parental gene, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000025976 | 6 retrocopies |
retro_itri_1757, retro_itri_1759, retro_itri_1778, retro_itri_1781, retro_itri_1782, retro_itri_186 ,
|