RetrogeneDB ID: | retro_rnor_1908 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 3:111743055..111743724(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Twf2 | ||
| Ensembl ID: | ENSRNOG00000048915 | ||
| Aliases: | None | ||
| Description: | twinfilin, actin-binding protein, homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1346078] |
Retrocopy-Parental alignment summary:
>retro_rnor_1908
GGCCACATCAAGGATGAGCTCTCCTTGGCTGGGTACCAGAAGCACCTGTCATCTTGTGCTGCACCTGCCCCACTGACTTC
AGCTGAGCGAGAGCTCCAGCAGATCCAAATCAATGAGGTGAAGACTGAGATCAGCGTGGAAAGCAAGCACCAGACCCTGC
AGGGCCTGGCCTTCCCCCTGCTGCCTGAGGCCCAGCGGGCACTTCAGCAACTCCAGCAGAAGACAGTCAACTATATCCAG
CTGAAGCTGGACCTGTAACGGGAGACCATCGAGCTGGTACACACAGAACCCACAAATGTGGCCCAGCTGCCCTCACGGGT
ACCCAGAGATGCTGCCCATTACCACTTCTTCCTGTACAAGCATACCCATGAGGGTGACTCCCTTGAATCTGTGGTGTTCA
TCTTCTCCAAGCCGGGGTACAAGTGCAGCATTAAGGAGCGCATGCTCTATTCCAGCTGCGAAAGCTGCCTCCTTGACTCT
GTAGAGCAAGACTTCCAGCTGGAGATCGCTAAGAAGATTGAGATCGGCGATGGGGCGGAGCTGACCGCTGAGTTCCTCTA
TGATGAAGTGCATCCCAAGCAGCACGCCTTCAAGCAGGCATTCTCCAAGCCCAAAGACCCTGGAGGCAAGCAGGGCCACA
AGCGCCTTATCCGCGGCCCCGGGGAGAAT
ORF - retro_rnor_1908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.27 % |
| Parental protein coverage: | 63.9 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GTVKDDLSLAGYQKHLSSCAAPAPLTSAERELQQIRINEVKTEISVESKHQTLQGLAFPLQPEAQRALQQ |
| G..KD.LSLAGYQKHLSSCAAPAPLTSAERELQQI.INEVKTEISVESKHQTLQGLAFPL.PEAQRALQQ | |
| Retrocopy | GHIKDELSLAGYQKHLSSCAAPAPLTSAERELQQIQINEVKTEISVESKHQTLQGLAFPLLPEAQRALQQ |
| Parental | LKQKTVNYIQLKLDLERETIELVHTEPTNVAQLPSRVPRDAARYHFFLYKHTHEGDSLESVVFIYSMPGY |
| L.QKTVNYIQLKLDL.RETIELVHTEPTNVAQLPSRVPRDAA.YHFFLYKHTHEGDSLESVVFI.S.PGY | |
| Retrocopy | LQQKTVNYIQLKLDL*RETIELVHTEPTNVAQLPSRVPRDAAHYHFFLYKHTHEGDSLESVVFIFSKPGY |
| Parental | KCSIKERMLYSSCKSRLLDSVEQDFQLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAFAKPKGPGGK |
| KCSIKERMLYSSC.S.LLDSVEQDFQLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAF.KPK.PGGK | |
| Retrocopy | KCSIKERMLYSSCESCLLDSVEQDFQLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAFSKPKDPGGK |
| Parental | RGHKRLIRGPGEN |
| .GHKRLIRGPGEN | |
| Retrocopy | QGHKRLIRGPGEN |
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 |
|---|---|---|
| SRP017611_brain | 0 .14 RPM | 23 .87 RPM |
| SRP017611_kidney | 0 .14 RPM | 4 .61 RPM |
| SRP017611_liver | 0 .07 RPM | 1 .41 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1908 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1908 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1908 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000022507 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000048915 | 2 retrocopies |
retro_rnor_1740, retro_rnor_1908 ,
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