RetrogeneDB ID: | retro_sscr_660 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 2:10754655..10755076(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C1D | ||
| Ensembl ID: | ENSSSCG00000008354 | ||
| Aliases: | None | ||
| Description: | C1D nuclear receptor corepressor [Source:HGNC Symbol;Acc:29911] |
Retrocopy-Parental alignment summary:
>retro_sscr_660
GTGTCTGGGGAAGAAACTAATAAAGACTATTCAGTAGAAATTCATGAGGGTTTATCAACTTTTGATAACTCCGTGGGTTC
TCTGGATGAGATGCTGACAACCATGTCTGTTTCTAGAAATGAATTGTTGCAGACGTTGGACCCACTTGAACAAGTGAAAG
TGGATTTAGTTTCTGTTTACACATTAAATTTAATATTTGGGGTTTATTTGGCAACTCGGGGAGTGAATCCTAAGGAACAT
CCAGTAAAGCAGGAATTGGAAAGAACCAGAGTATACATGAACAGAGTGAAGGAAGTAACAGACAAGAAAAAGGCTGGCAA
GCTGGGCAGAGGCACAGCTTCAAGATTGGTTAAAAAATGCCCTCTGGGAACCAAAACCTAAAAATGCATGCAAAGTTGCC
AGTAAAGGAAAAAGTAAAAAT
ORF - retro_sscr_660 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.72 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGEEINEDYPVEIHECLSTFENSIGAVDEMLKTMMSVSRNELLQKLDPLEQAKVDLVSAYTLNSMFWVY |
| ..GEE.N.DY.VEIHE.LSTF.NS.G..DEML.TM.SVSRNELLQ.LDPLEQ.KVDLVS.YTLN..F.VY | |
| Retrocopy | VSGEETNKDYSVEIHEGLSTFDNSVGSLDEMLTTM-SVSRNELLQTLDPLEQVKVDLVSVYTLNLIFGVY |
| Parental | LATQGVNPKEHPVKQELGKINLVLNIIRESFLESLVGMLQRGAASRFV-KNALWEPKPKNASKVANKGKS |
| LAT.GVNPKEHPVKQEL.......N...E.......G.L.RG.ASR.V.KNALWEPKPKNA.KVA.KGKS | |
| Retrocopy | LATRGVNPKEHPVKQELERTRVYMNRVKEVTDKKKAGKLGRGTASRLV>KNALWEPKPKNACKVASKGKS |
| Parental | KN |
| KN | |
| Retrocopy | KN |
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 | 2 .92 RPM |
| SRP014902_testis | 0 .00 RPM | 6 .22 RPM |
| SRP018288_heart | 0 .00 RPM | 9 .12 RPM |
| SRP018288_kidney | 0 .00 RPM | 9 .46 RPM |
| SRP018288_liver | 0 .00 RPM | 4 .48 RPM |
| SRP018288_lung | 0 .00 RPM | 14 .87 RPM |
| SRP018856_adipose | 0 .00 RPM | 7 .34 RPM |
| SRP035408_brain | 0 .00 RPM | 5 .21 RPM |
| SRP035408_liver | 0 .00 RPM | 7 .81 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_660 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_660 was not experimentally validated.