RetrogeneDB ID: | retro_itri_1225 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393406.1:5374824..5375416(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NIT1 | ||
| Ensembl ID: | ENSSTOG00000006372 | ||
| Aliases: | None | ||
| Description: | nitrilase 1 [Source:HGNC Symbol;Acc:7828] |
Retrocopy-Parental alignment summary:
>retro_itri_1225
GCATTTGATTTCACTGCACAAGACCCTACAGAGACACTGTGCCTGTCTGAGCCTGTGGGTGGGAACCTTCTGGGGGAATA
CACCCAGCTTTAAAGGAATGTGTGGACTCTGGCTGTCCTTGGGTGGTTTCCATGAGCGTGGCCAAGACTGGGAGCAGACT
CAGAGAATCTACAACTGTCATGTGCTTCTGAACAGCAAGGGATCAAGAGTGGTACCTATAGGAAGTCGTATCTGTGTGAT
GTAGAGATTCTAGGGCAGGAGCCTATCCAAGAAAGCAATTTTACCATGCCTGGGCCCAGTCTTGAGTCACCGTCAGCACA
CCAGCAGGCAAGATTGATCTAGCTGTCTGTGGTTCCCTCAACTCTCTAGCATTGGCTCACACTGGAGCAGAAATATTCAC
CTACCCTTCAGCTTTTGGATCTGCTACAGGCCCTATCCACTGGGAAGTATTGCTGAGCTATGCTATTGAAACCCAGTGCT
ATGTTGTGGCAGCTGCATAGTGTGGACACCACCATGAGAAGAGAGCAAGTTATGGCCACAGCATGGTAGTAGCCCTTGGG
GAACAGTGGTGGCCCATTGCTCTGAAGAGCCT
ORF - retro_itri_1225 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.33 % |
| Parental protein coverage: | 67.67 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | AFDYIARDPAESLSLSEPLSGNLLGEYTQLARE-CGIWLSLGGFHERGQDWEQTQKIYNCHVLLNSKGSI |
| AFD..A.DP.E.L.LSEP..GNLLGEYTQL.R..CG.WLSLGGFHERGQDWEQTQ.IYNCHVLLNSKGS. | |
| Retrocopy | AFDFTAQDPTETLCLSEPVGGNLLGEYTQL*RN>CGLWLSLGGFHERGQDWEQTQRIYNCHVLLNSKGSR |
| Parental | V-ATYRKTHLCDIEIPGQEPMRESNSTLPGSSLESP-VSTPAGKIGLAVCYDIRFPELSLALAQAGAEIL |
| V..TYRK..LCD.EI.GQEP..ESN.T.PG.SLESP.VSTPAGKI.LAVC........SLALA..GAEI. | |
| Retrocopy | V<GTYRKSYLCDVEILGQEPIQESNFTMPGPSLESP<VSTPAGKIDLAVCGSLN----SLALAHTGAEIF |
| Parental | TYPSAFGSVTGPAHWEVLLRARAIETQCYVVAAAQCGRHHEKRASYGHSMVV-DPWGTVVARCSEGP |
| TYPSAFGS.TGP.HWEVLL...AIETQCYVVAAA.CG.HHEKRASYGHSMVV..PWGTVVA.CSE.P | |
| Retrocopy | TYPSAFGSATGPIHWEVLL-SYAIETQCYVVAAA*CGHHHEKRASYGHSMVV<SPWGTVVAHCSEEP |
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_1225 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1225 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 | ENSSTOG00000006372 | 1 retrocopy |
retro_itri_1225 ,
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