RetrogeneDB ID: | retro_itri_1426 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393483.1:1278371..1278779(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HLA-DOB | ||
| Ensembl ID: | ENSSTOG00000003405 | ||
| Aliases: | None | ||
| Description: | major histocompatibility complex, class II, DO beta [Source:HGNC Symbol;Acc:4937] |
Retrocopy-Parental alignment summary:
>retro_itri_1426
CTGCATCAGCACAACCTCTGCTCCATGACAGGCTTCTATCCAGGGGACATAAAGACCAGGTGGTTCTGGAATGGACAGGA
GGAGAGAGCTGGCATTATGTCCACTGGTCTTATTAGGAATGGAGACTGGACCTTTCAGACCATAGTGATGCTGGAAGCGA
CTCCTTCATCTGGAGATGTTTACAGCTGTCTTGTTGAGCACCCCAGTCTGTTGAGCCCTGTTTCTGTGGAGTGGAGAGAT
CAGTATGAATATTCTTGGAAAAAGATACCAAATGGAGTTGGAGCCTTCCTGCTTGGGCTAATTGTCCTTATGGTGGGGAT
TGTCATCCACCTCAGGGCTAGGAAAGGATCTGTGGAGACTCAGTCTGGTGATGAGGTCTCAAGAGCTATTCCACAGCAGC
CATACTCA
ORF - retro_itri_1426 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.61 % |
| Parental protein coverage: | 50.74 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LHQHNLLLCSVTGFYPGDIKIRWFWNGQEERAGVLSTGLIRNGDWTFQTMVMLEVTPSPGDVYSCLVEHP |
| LHQHNL..CS.TGFYPGDIK.RWFWNGQEERAG..STGLIRNGDWTFQT.VMLE.TPS.GDVYSCLVEHP | |
| Retrocopy | LHQHNL--CSMTGFYPGDIKTRWFWNGQEERAGIMSTGLIRNGDWTFQTIVMLEATPSSGDVYSCLVEHP |
| Parental | SLPGPVSVEWRAQREYSWKKILSGVGAFLLGLTFLLVGIIIHLRARKGSVETQSGDKISRAILQKPNS |
| SL..PVSVEWR.Q.EYSWKKI..GVGAFLLGL..L.VGI.IHLRARKGSVETQSGD..SRAI.Q.P.S | |
| Retrocopy | SLLSPVSVEWRDQYEYSWKKIPNGVGAFLLGLIVLMVGIVIHLRARKGSVETQSGDEVSRAIPQQPYS |
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_1426 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1426 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 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000003405 | 1 retrocopy |
retro_itri_1426 ,
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