RetrogeneDB ID: | retro_sscr_710 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 3:100941085..100941465(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000030295 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_710
ATGGGAGACAAGCCAGTTTGAGAGCAGACTGGATCCAGCTTCATTCAACATTACTACCAGTTATTTGATAACGACAGAAC
CCAACTAGGCACAATTTATAGTGACGTGTCCTGCCTTCCATGGGAAGGACAGCAATTCCAGGGGAAAACTGCCCTTGCGG
AGAAATTATCTAGCCTTCTGTTCCAGGAAACCCAGCATAGCATCACAGCGCAGGACCATCAGCCCACACCAGACAGCTGC
ATCATCAGCATGGGTGTGCACCAGCTCAAGGCCAATGAAGACCCCATGATGGGGTCCACCAGATGTTCCTATTAAAGAAC
ATCAACGATGCTTGTGTTTGCACCAATGACCTGGTCAGGCTTGTCCTGCACAACTTCGGC
ORF - retro_sscr_710 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.81 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKTAIVEKLSSLPFQKIQHSITA |
| MGDKP..EQ.GSSFIQHYYQLFDNDRTQLG.IY.D.SCL.WEGQQFQGKTA..EKLSSL.FQ..QHSITA | |
| Retrocopy | MGDKPV*EQTGSSFIQHYYQLFDNDRTQLGTIYSDVSCLPWEGQQFQGKTALAEKLSSLLFQETQHSITA |
| Parental | QDHQPTPDSCIISMVVGQLKADEDPIM-GFHQMFLLKNINDAWVCTNDMFRLALHNFG |
| QDHQPTPDSCIISM.V.QLKA.EDP.M.G.HQMFLLKNINDA.VCTND..RL.LHNFG | |
| Retrocopy | QDHQPTPDSCIISMGVHQLKANEDPMM<GVHQMFLLKNINDACVCTNDLVRLVLHNFG |
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 | 43 .40 RPM |
| SRP014902_testis | 0 .14 RPM | 20 .09 RPM |
| SRP018288_heart | 0 .03 RPM | 27 .92 RPM |
| SRP018288_kidney | 0 .00 RPM | 27 .68 RPM |
| SRP018288_liver | 0 .00 RPM | 17 .91 RPM |
| SRP018288_lung | 0 .00 RPM | 67 .51 RPM |
| SRP018856_adipose | 0 .18 RPM | 17 .94 RPM |
| SRP035408_brain | 0 .03 RPM | 20 .52 RPM |
| SRP035408_liver | 0 .00 RPM | 12 .62 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_710 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_710 was not experimentally validated.