RetrogeneDB ID: | retro_itri_779 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393321.1:29540..30159(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MSI1 | ||
| Ensembl ID: | ENSSTOG00000009799 | ||
| Aliases: | None | ||
| Description: | musashi RNA-binding protein 1 [Source:HGNC Symbol;Acc:7330] |
Retrocopy-Parental alignment summary:
>retro_itri_779
GACTTTTTTAGCAAATTTGGAGAAATTAGAGAATGCATGGTCGTGAGAGATGCCACTACAAAATGCTTCAGAGGCCTCAG
TCATGCCAGTTAATATATCCACCAAGTGTAGATAAAGTATTATGTCCACCCCACTATGAGTTAGATTCCAAGATGACTGA
CCCCAAACTTGCATTTCTTCCCAGAGTGCAATCCAAGATGATGACAACAACAAAGAAAGTATTTTTAGGCAGATTATCTG
TGAACACAGTAGTGGAAGATGTAAAGCAATATTTTGAGTAGTCTGGCAAGGTAGAAGATGCAATGCTTATGTTTGATAAA
TCCACCAACAGGCGCAGAGGGTTTGGCTTCATCACTTTGGAGAATGAATATGTTGTGGAGAAAGTTTGTGAGATTCATTT
CTGTAAGATCCATAATAAAATGGTAAACCACAAGAAAAATCCACCCAAAGAAGCCCTGTTGTTCCCACCTGGGACAAGAG
TCCAGGCAGGGAACTGCCTTACACCATGGATGTGTTGCTAGTCCTCCTGGGGTTGAAGGTCTACCCCAGCTTTATGGAAA
TTTACAGTGGAGGCTACCCTGGACTTGCTCCTGGCTTCAGCTATCAGTTCCCTGAATAT
ORF - retro_itri_779 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.5 % |
| Parental protein coverage: | 65.72 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EYFGQFGEVKECLVMRDPLTKRSRGFGFVT-FMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVT |
| ..F..FGE..EC.V.RD..TK..RG............VDKVL.....ELDSK..DPK.AF..R.Q.KM.T | |
| Retrocopy | DFFSKFGEIRECMVVRDATTKCFRGLSHAS<LIYPPSVDKVLCPPHYELDSKMTDPKLAFLPRVQSKMMT |
| Parental | RTKKIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINN |
| .TKK.F.G.LSVNT.VEDVKQYFE..GKV.DAMLMFDK.TNR.RGFGF.T.E.E..VEKVCEIHF..I.N | |
| Retrocopy | TTKKVFLGRLSVNTVVEDVKQYFE*SGKVEDAMLMFDKSTNRRRGFGFITLENEYVVEKVCEIHFCKIHN |
| Parental | KMVECKKAQPKEVMSPTGSARGRS-RVMPYGMDAFMLGIGMLGYPGFQATTYASRSYTGLAPGYTYQFPE |
| KMV..KK..PKE........R....R..PY.MD......G...YP.F......S..Y.GLAPG..YQFPE | |
| Retrocopy | KMVNHKKNPPKEALLFPPGTRVQA<RELPYTMDVLLVLLGLKVYPSFM--EIYSGGYPGLAPGFSYQFPE |
| Parental | F |
| . | |
| Retrocopy | Y |
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_779 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_779 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000010283 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000009799 | 1 retrocopy |
retro_itri_779 ,
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