RetrogeneDB ID: | retro_itri_1835 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393973.1:45456..46136(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM120A | ||
| Ensembl ID: | ENSSTOG00000021804 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 120A [Source:HGNC Symbol;Acc:13247] |
Retrocopy-Parental alignment summary:
>retro_itri_1835
CCACCAGAATTCTCACTAGTGATCATGAAGGAATGGGCAGCTTACAAGGGGCAATCTCCTCCAACCAAGTCTCAGGGCAG
GGGCAGAGGCTTTGCAGGAGTCTGTGGCTTTGGCAGCCCTTATGGGAAAACCATAGCAACTGGCCCTTACCATGCCTTCT
GGGTGGAGGCAGCATCAGAACACTGTGGAGCCTTCTTAGGCACTGACAGCAGTGAAACTAGCAAGTCCCAGGGTGGAGTC
CAAACTATACCTTCTCAGGGAGGGAAACTAGAAATCGCTGGCACTGTGGTTGGACACTGGGCAGGAAGCAGGCAGGGCTG
TGGAGTCTGAGGGCCCTTCCCATTGCAAGTGGTCTCTGTCGGAGGAACAACAAGAGGGCATCCAATAGGAGTTATTTCCA
TCCTAGAAATACAGAGGTTTGGTAGAGTTGGAAGGCACTATGGCCGAGGTTGTAAAAGCCAGGGAGCAATTCAGGGCAGA
CCTCCTTATGCTGCTTCAGAGGAAGAAGTGGCCAAAGAGCTGAAGTCAAAATCTGGGGAATCAAAGTCCTTTGCCATGTC
TTCACACGGGTCCCTGCCTGAAAATGCAGTGATGGCCGAGGAAAAGCCAGTACCCCAGATGAATGAAAGTGCAGGGGACA
CCAGGGCCCCCAGCCACTCAAAAGTGCCTTGAACAATGAC
ORF - retro_itri_1835 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.88 % |
| Parental protein coverage: | 55.42 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PPALPFYPASVYPRHFGPVPP--SQGRGRGFAGVCGFGGPYGETVASGPYRAFRVAAASGHCGAFSGSDS |
| PP..............G..PP..SQGRGRGFAGVCGFG.PYG.T.A.GPY.AF.V.AAS.HCGAF.G.DS | |
| Retrocopy | PPEFSLVIMKEWAAYKGQSPPTKSQGRGRGFAGVCGFGSPYGKTIATGPYHAFWVEAASEHCGAFLGTDS |
| Parental | SRTSKSQGGVQPIPSQGGKLEIAGTVVGHWAGSRRGRGGRGPFPLQVVSVGGPARGRPRGVISTPVIRTF |
| S.TSKSQGGVQ.IPSQGGKLEIAGTVVGHWAGSR.G.G..GPFPLQVVSVGG..RG.P.GVIS...I..F | |
| Retrocopy | SETSKSQGGVQTIPSQGGKLEIAGTVVGHWAGSRQGCGV*GPFPLQVVSVGGTTRGHPIGVISILEIQRF |
| Parental | GRGGRYYGRGYKSQGAIQGRPPYAASAEEVAKELKSKSGESKSSAVSSDGSLAENGVMAEEKPVPQMNGS |
| GR.GR.YGRG.KSQGAIQGRPPYAAS.EEVAKELKSKSGESKS.A.SS.GSL.EN.VMAEEKPVPQMN.S | |
| Retrocopy | GRVGRHYGRGCKSQGAIQGRPPYAASEEEVAKELKSKSGESKSFAMSSHGSLPENAVMAEEKPVPQMNES |
| Parental | AGDTRAPSHS-ESALNND |
| AGDTRAPSHS..SALNND | |
| Retrocopy | AGDTRAPSHS<KSALNND |
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_1835 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1835 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000021804 | 2 retrocopies |
retro_itri_1835 , retro_itri_1883,
|