RetrogeneDB ID: | retro_itri_516 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393298.1:3095460..3095952(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSTOG00000021736 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMACHC | ||
| Ensembl ID: | ENSSTOG00000006090 | ||
| Aliases: | None | ||
| Description: | methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria [Source:HGNC Symbol;Acc:24525] |
Retrocopy-Parental alignment summary:
>retro_itri_516
TTTGGCTTCGGGGTTTACCCCTTCCAGGTGGCATGGTACAATGAGCTTCTGCCTCCAGCCTTCCACCTGCCCCTGCCAGG
ACCTACCCTGGCCTTCTTGGTACACAGCACACCGACCAAGTTTGACCAGGCCCTTAAGCCCTTCTTGCAGAGCCGCCACC
TCCAACCACTAACTGACCCTGTGGATCAGTGTGTGGCCTACCACCTGAGACGTGTTAGACAGAGCCTCCCAGAGCTGCAG
ATGGAAATCATTGCTGACTACAAGGTATACCCCAACTGGCGCCCTAAGATTCTGGCCCAGACAGCAGCCCATGTGGCAGG
AGCTGCTTATTACTACCAATGCCAAGATGTGGAAGCTGACCCATGGGGAACTCAGCACATAGCAGGTGTGTGCATACACC
CCCGATTTGGGGGCTTGTTTGCCATCCGAGGTGTCGTGCTGCTGCCAGGGACAGACGCCAGATCTGCCACGGAGAAAGCC
CCCTGACTGTGT
ORF - retro_itri_516 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.2 % |
| Parental protein coverage: | 58.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FGFEVYPFQVAWYNELLPPAFHLPLPGPTLAFLVLSTPAMFDQALKPFLQSHHLQSLTDPVDQCVAYHLR |
| FGF.VYPFQVAWYNELLPPAFHLPLPGPTLAFLV.STP..FDQALKPFLQS.HLQ.LTDPVDQCVAYHLR | |
| Retrocopy | FGFGVYPFQVAWYNELLPPAFHLPLPGPTLAFLVHSTPTKFDQALKPFLQSRHLQPLTDPVDQCVAYHLR |
| Parental | RVRQSLPELQMEVIADYEVYPNRRPKILAQTAAHVAGAAYYYQRQDVEADPWGTQHIAGVCIHPRFGGWF |
| RVRQSLPELQME.IADY.VYPN.RPKILAQTAAHVAGAAYYYQ.QDVEADPWGTQHIAGVCIHPRFGG.F | |
| Retrocopy | RVRQSLPELQMEIIADYKVYPNWRPKILAQTAAHVAGAAYYYQCQDVEADPWGTQHIAGVCIHPRFGGLF |
| Parental | AIRGVVLLPGTETPDLPRKKPPDC |
| AIRGVVLLPGT.......K.P..C | |
| Retrocopy | AIRGVVLLPGTDARSATEKAP*LC |
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_516 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_516 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 | ENSSTOG00000006090 | 1 retrocopy |
retro_itri_516 ,
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