RetrogeneDB ID: | retro_rnor_1579 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 2:248399805..248399997(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Gypc | ||
| Ensembl ID: | ENSRNOG00000029939 | ||
| Aliases: | Gypc, GPC | ||
| Description: | Glycophorin-C [Source:UniProtKB/Swiss-Prot;Acc:Q6XFR6] |
Retrocopy-Parental alignment summary:
>retro_rnor_1579
ATGAGCATCCCTGTCAGCAAACCATCTCCTGAGCGCCTCAAGCCTAACCCAATGATATCCTGCAGCATTATGGAGATTGC
CACCATTGCAGCTGAGATCACTGCTGTGGCCTTGTTCTTGGTCTGCCTTCTCTTTCTCATGCTTCGATACCTGTACAGGC
ACAAGGGCACCTACCACACCAATGAGGCCAAA
ORF - retro_rnor_1579 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.12 % |
| Parental protein coverage: | 67.37 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSSPVRTPPPERLEPNPGMSYAVMEIAIIAAVITAVALVLVCLLFLMLRYLYRHKGTYYTNEAK |
| MS.PV..P.PERL.PNP..S...MEIA.IAA.ITAVAL.LVCLLFLMLRYLYRHKGTY.TNEAK | |
| Retrocopy | MSIPVSKPSPERLKPNPMISCSIMEIATIAAEITAVALFLVCLLFLMLRYLYRHKGTYHTNEAK |
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 | 5 .75 RPM |
| SRP017611_kidney | 0 .00 RPM | 9 .42 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .40 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1579 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1579 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1579 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000029939 | 1 retrocopy |
retro_rnor_1579 ,
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