RetrogeneDB ID: | retro_sscr_405 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 14:15207047..15207442(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SNRPN | ||
| Ensembl ID: | ENSSSCG00000028124 | ||
| Aliases: | None | ||
| Description: | small nuclear ribonucleoprotein polypeptide N [Source:HGNC Symbol;Acc:11164] |
Retrocopy-Parental alignment summary:
>retro_sscr_405
ATGGCTGTGGGCAAGGGCAGGACGATGGTCAGCATGTGGCCCACAGAACAAGATGGCACCTACTGGATAACCTCATCTTC
ACTGGCATCTTCGAGGCTTCCACAGCATGTGAGCTGACCCTCTGTGATTGTGACAGGTTCAAGAAGACCAAATCAAAGAA
TGTGAAACAGCCAGAGTGTAGAAGGTGGGTGCTGGATCTGGTGTGCCTGCATGGGGAGAATCTGGTTTCCATGACTATCC
CGGGCCACCCCAAAGTTACTGTCAAGGCTTGGGTACCACTTGCTGGAGCTGAAGGAGGTTCTGCATTTGGCAGGGCAGCC
AACAGAAGAGTATCAAGTCCCCAGGCTTTTGCTGGGTTAGGACACCATTCAAGGGAATGAGGGACATCCCAACAG
ORF - retro_sscr_405 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.43 % |
| Parental protein coverage: | 57.92 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTVGKSSKML-QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNAKQPEREEKRVLGL |
| M.VGK...M..QH...R.R..L.D..IF.G.F.A......L.LCDCD.F.K.K.KN.KQPE.....VL.L | |
| Retrocopy | MAVGKGRTMV<QHVAHRTRWHLLDNLIFTGIFEA-STACELTLCDCDRFKKTKSKNVKQPEC-RRWVLDL |
| Parental | VLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPVRGVGGPSQ |
| V.L.GENLVSMT..G..PK.T..A.VPLAGA.GG...GRAA.R.V......PQA.AGL....R..G...Q | |
| Retrocopy | VCLHGENLVSMTIPG-HPKVTVKAWVPLAGAEGGSAFGRAANRRVSS----PQAFAGLGHHSRE*GTSQQ |
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 | 12 .48 RPM |
| SRP014902_testis | 0 .00 RPM | 44 .98 RPM |
| SRP018288_heart | 0 .00 RPM | 50 .13 RPM |
| SRP018288_kidney | 0 .00 RPM | 72 .70 RPM |
| SRP018288_liver | 0 .00 RPM | 4 .64 RPM |
| SRP018288_lung | 0 .00 RPM | 17 .21 RPM |
| SRP018856_adipose | 0 .00 RPM | 27 .18 RPM |
| SRP035408_brain | 0 .00 RPM | 436 .17 RPM |
| SRP035408_liver | 0 .00 RPM | 18 .08 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_405 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_405 was not experimentally validated.