RetrogeneDB ID: | retro_sscr_1113 | ||
Retrocopylocation | Organism: | Pig (Sus scrofa) | |
| Coordinates: | GL895603.2:12830..13150(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | NME4 | ||
| Ensembl ID: | ENSSSCG00000007986 | ||
| Aliases: | None | ||
| Description: | NME/NM23 nucleoside diphosphate kinase 4 [Source:HGNC Symbol;Acc:7852] |
Retrocopy-Parental alignment summary:
>retro_sscr_1113
CCCCAGGCCAAGCCTGCTCCCAGCTTAGGAGGGCCCTCTTGGACCCAGAAGCAGACCCTGGTGGTGGTAAAGCTAGATGG
GGGCAGCAGCAGCTCCTTGGGGATGGGATCCAGCCTTTGGAGAGGCTGGGCTTCCCGTTGGTGGGGATGAAGGGGCTGCA
GGCACCAGTGGGCATCCTTGCTGAACACTCCAGCGACCTGCAGAGGAAGCCCTGCCACCAAGCGCTCATCATCTACCTGA
GCTCCGGTTCCCTGGAGGCCATGGTCTGGGACAACCTCACTGTGGTCCACACCTCTGGGGCTACAATGCAACACACCAGC
CCCCAGGCCAAGCCTGCTCCCAGCTTAGGAGGGCCCTCTTGGACCCAGAAGCAGACCCTGGTGGTGGTAAAGCTAGATGG
GGGCAGCAGCAGCTCCTTGGGGATGGGATCCAGCCTTTGGAGAGGCTGGGCTTCCCGTTGGTGGGGATGAAGGGGCTGCA
GGCACCAGTGGGCATCCTTGCTGAACACTCCAGCGACCTGCAGAGGAAGCCCTGCCACCAAGCGCTCATCATCTACCTGA
GCTCCGGTTCCCTGGAGGCCATGGTCTGGGACAACCTCACTGTGGTCCACACCTCTGGGGCTACAATGCAACACACCAGC
ORF - retro_sscr_1113 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.78 % |
| Parental protein coverage: | 57.22 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PRLCARPNSGCPSWTRERTLVAVKPDGV-QRRLVGDVIQRFERRGFKLVGMKMLQVPESLLAEHYHELRR |
| P.....P..G.PSWT...TLV.VK.DG..Q..L.GD.IQ..ER.GF.LVGMK.LQ.P...LAEH...L.R | |
| Retrocopy | PQAKPAPSLGGPSWTQKQTLVVVKLDGG<QQQLLGDGIQPLERLGFPLVGMKGLQAPVGILAEHSSDLQR |
| Parental | KPFYPALISYMSSGPVVAMVWEGPNVVCASRAMIGHTN |
| KP...ALI.Y.SSG...AMVW....VV..S.A...HT. | |
| Retrocopy | KPCHQALIIYLSSGSLEAMVWDNLTVVHTSGATMQHTS |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 0 .66 RPM |
| SRP014902_testis | 0 .14 RPM | 2 .26 RPM |
| SRP018288_heart | 0 .00 RPM | 0 .18 RPM |
| SRP018288_kidney | 0 .00 RPM | 1 .77 RPM |
| SRP018288_liver | 0 .00 RPM | 0 .16 RPM |
| SRP018288_lung | 0 .00 RPM | 1 .63 RPM |
| SRP018856_adipose | 0 .00 RPM | 0 .83 RPM |
| SRP035408_brain | 0 .03 RPM | 2 .51 RPM |
| SRP035408_liver | 0 .00 RPM | 0 .32 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1113 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1113 was not experimentally validated.