RetrogeneDB ID: | retro_cfam_555 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 13:47983176..47983845(+) | ||
| 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: | ENSCAFG00000010283 | ||
| Aliases: | None | ||
| Description: | musashi RNA-binding protein 1 [Source:HGNC Symbol;Acc:7330] |
Retrocopy-Parental alignment summary:
>retro_cfam_555
AAAATGTTTATCGGCGGACTAAGCTGGCAGACCTCACCAGATAGCCTTAGAGACTATTTTAGCAAATTTGGAGAAATTAG
AGAATGTATGGTCATGAGAGATCCCACTACGAAACGCTCCAGAGGCTTCGGTTTCGTCACGTTCGCAGATCCAGCAAGTG
TAGATAAAGTATTAGGTCAGCCCCACCATGAGTTAGATTCCAAGACGATTGATCCTAAAGTTGCATTTCCTCGTCGGGCA
CAACCCAAGATGGTCACAAGAACAAAGAAAATATTTGTAGGCGGATTATCTGCGAACACAGTGGTGGAAGATGTAAAGCA
ATACTTTGAGCAGTTTGGCAAGGTGGAGGACGCAATGCTGATGTTTGATAAGACAACCAACAGGCACAGAGGGTTTGGCT
TTGTCACGTTTGAGAATGAAGATGTTGTGGAGAAAGTCTGTGAGATTCATTTCCATGAAATCAATAATAAAATGGTAGAA
TGTAAGAAAGCTCAGCCTAAGGAAGTCATGTTCCCACCGGGGACAAGAGGCCGGGCCCGGGGACTGCCTTATACCATGGA
CGCGTTCATGCTTGGCATGGGAATGCTAGGCTACCCCAACTTTGTGGCAACCTATGGCCGCGGCTACCCTGGATTTGCTC
CTAGCTATGGTTATCAGTTCCCAGACTAC
ORF - retro_cfam_555 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.09 % |
| Parental protein coverage: | 62.43 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI |
| KMFIGGLSWQT....LR.YF..FGE..EC.VMRDP.TKRSRGFGFVTF.D.A.VDKVL.Q..HELDSKTI | |
| Retrocopy | KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTI |
| Parental | DPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKQYFEQFEKVDDAMLMFDKTTNRHRGFGFVTFESE |
| DPKVAFPRRAQPKMVTRTKKIFVGGLS.NT.VEDVKQYFEQF.KV.DAMLMFDKTTNRHRGFGFVTFE.E | |
| Retrocopy | DPKVAFPRRAQPKMVTRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENE |
| Parental | DIVEKVCEIHFHEINNKMVECKKAQPKEVMSPTGSARGRSRVMPYGMDAFMLGIGMLGYPGFQATTYASR |
| D.VEKVCEIHFHEINNKMVECKKAQPKEVM.P.G..RGR.R..PY.MDAFMLG.GMLGYP.F.AT....R | |
| Retrocopy | DVVEKVCEIHFHEINNKMVECKKAQPKEVMFPPGT-RGRARGLPYTMDAFMLGMGMLGYPNFVAT--YGR |
| Parental | SYTGLAPGYTYQFPEF |
| .Y.G.AP.Y.YQFP.. | |
| Retrocopy | GYPGFAPSYGYQFPDY |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP012049_cerebellum | 18 .90 RPM | 56 .78 RPM |
| SRP017611_brain | 7 .30 RPM | 7 .94 RPM |
| SRP017611_kidney | 14 .59 RPM | 3 .37 RPM |
| SRP017611_liver | 2 .32 RPM | 0 .00 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_555 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_555 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_555 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000010283 | 1 retrocopy |
retro_cfam_555 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000009799 | 1 retrocopy |