RetrogeneDB ID: | retro_rnor_1815 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 3:116906707..116906966(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | H2afv | ||
| Ensembl ID: | ENSRNOG00000007026 | ||
| Aliases: | LOC685909, H2A.Z-2, H2afv | ||
| Description: | H2A histone family, member V [Source:RefSeq peptide;Acc:NP_001099489] |
Retrocopy-Parental alignment summary:
>retro_rnor_1815
TTGGTTGGAGGCAAAGCTGAAAAAGACAGTGGGAAGGCCAAGGTTAAGGCAGTGTCTCCATAACAGAAAGCTGGGCTCCA
GTTTCCTGTGGGCCGCATCTACAGACACTTGAAGACTCGCACCACAAGCCGTGGATACCTGTGGGCCACATTGCTGCTGT
GTTCAGAGCTGCAATTCTGTGAGTACCTCACAGCTGAGGTGTTGGGGTTGGCAGGTAAATGCTTCTAAAGATCTCAAAGT
AAAGCGAGTCACTTACAGG
ORF - retro_rnor_1815 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.26 % |
| Parental protein coverage: | 66.41 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGGKAGKDSGKAKAKAVSRSQRAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS-AAILEYLTAEVLEL |
| ..GGKA.KDSGKAK.KAVS..Q.AGLQFPVGRI.RHLKTRTTS.G...AT....S.....EYLTAEVL.L | |
| Retrocopy | LVGGKAEKDSGKAKVKAVSP*QKAGLQFPVGRIYRHLKTRTTSRGYLWATLLLCSELQFCEYLTAEVLGL |
| Parental | AG-NASKDLKVKRITPR |
| AG.NASKDLKVKR.T.R | |
| Retrocopy | AG>NASKDLKVKRVTYR |
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 .00 RPM | 9 .42 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .93 RPM |
| SRP017611_liver | 0 .00 RPM | 5 .92 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1815 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1815 was not experimentally validated.