RetrogeneDB ID: | retro_sscr_523 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 16:37195127..37195718(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNFT1 | ||
| Ensembl ID: | ENSSSCG00000017671 | ||
| Aliases: | None | ||
| Description: | ring finger protein, transmembrane 1 [Source:HGNC Symbol;Acc:30206] |
Retrocopy-Parental alignment summary:
>retro_sscr_523
CCCTATATTTTGATTCTGAGTGTCAAGCCTGTTACAACAGGAATTGCTCTTGGAACTGCACGACTTACAACTTCTATATA
TGCAAACAAAAGCATTTTAAATCAGGTTCTTCTAAAAGAAAGGCACTTGGAGATTGTGCCTTTTTTACTGGTATTCCTAG
CAGGATCTTCTGTTCTTTCATATCGCACCTTTCATTCTCAGTCATTTTACTACAGCTTAATTTTTTAAAATCCCATTTTG
GACAATGTGAGCTTCTGGGAAGTACTTTGGATTGTTGGAATCACAGACTTCATTGTGAAATTCCTCTTCATGGGCTTAAA
ATGTCTTATTTTATTGGTGCCTTCTTTTATCATGCCTTTTAAATCCAAGGTTTACTGGTATATGCTTTTAGAAGAATTAT
GTCAGTATTACCAAACACTTATTCCCATTCCAGTTTGGTTTCATTACCTTATAAACTATGAGGAGTTTGATAATGTAACT
AGATGGAGTCTAGGGATATTGCTGGTTTTACTCAACCTCATACTAACACTTCCGGACTTTTTTGGACATCTAAGAACTTT
CAGATGGGTTTTGCGAATATTTTTTACACAG
ORF - retro_sscr_523 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.11 % |
| Parental protein coverage: | 56.3 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PYILILGVKLVMQHITGISLGIGLLTTFIYANKSIINQVFLRERCSKIQCAWLLVFLAGSSVLLYYTFHS |
| PYILIL.VK.V....TGI.LG...LTT.IYANKSI.NQV.L.ER...I....LLVFLAGSSVL.Y.TFHS | |
| Retrocopy | PYILILSVKPVT---TGIALGTARLTTSIYANKSILNQVLLKERHLEI-VPFLLVFLAGSSVLSYRTFHS |
| Parental | QSLYYSLIFLNPTLDYSSFWEVLWIVGITDFILKFLFMGLKCLILLVPSFVMPFKSKGYWYMLLEELCQY |
| QS.YYSLIF.NP.LD..SFWEVLWIVGITDFI.KFLFMGLKCLILLVPSF.MPFKSK.YWYMLLEELCQY | |
| Retrocopy | QSFYYSLIF*NPILDNVSFWEVLWIVGITDFIVKFLFMGLKCLILLVPSFIMPFKSKVYWYMLLEELCQY |
| Parental | YRTFVPIPVWFRYLISYGEFGNVTRWSLGILLALLYLILKLLDFFGHLKTFTRVLRIFFTR |
| Y.T..PIPVWF.YLI.Y.EF.NVTRWSLGILL.LL.LIL.L.DFFGHL.TF..VLRIFFT. | |
| Retrocopy | YQTLIPIPVWFHYLINYEEFDNVTRWSLGILLVLLNLILTLPDFFGHLRTFRWVLRIFFTQ |
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 | 8 .63 RPM |
| SRP014902_testis | 0 .00 RPM | 15 .98 RPM |
| SRP018288_heart | 0 .00 RPM | 22 .53 RPM |
| SRP018288_kidney | 0 .00 RPM | 29 .95 RPM |
| SRP018288_liver | 0 .00 RPM | 27 .98 RPM |
| SRP018288_lung | 0 .00 RPM | 9 .67 RPM |
| SRP018856_adipose | 0 .00 RPM | 11 .27 RPM |
| SRP035408_brain | 0 .00 RPM | 0 .95 RPM |
| SRP035408_liver | 0 .00 RPM | 5 .87 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_523 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_523 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_523 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009747 | 2 retrocopies | |
| Cavia porcellus | ENSCPOG00000014736 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000017671 | 2 retrocopies |
retro_sscr_1201, retro_sscr_523 ,
|