RetrogeneDB ID: | retro_sscr_970 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 8:69920600..69921206(+) | ||
| Located in intron of: | ENSSSCG00000029658 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000030310 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_970
TTTTACAAACTTGACTTATTAGCAGTAACGGTGGAGCTGGAGAGTATTGAGCCTTCTCCAAGCTGCAGAGCAAGTACCAC
CAATAGTGTGGTGGAACTTGTGGCCCAACCCAAGGCCGTGGCTCCTTCTACCTGCAGAAGTCAGCCCTCCCCTCTCCCTG
TGCTTGTGGACTGGTCTGGTGATCCACTGGGTGTCAGGATTTCTTCTGACAGCTTTATGGAATGGATCAATGAGGATAAC
CTCAAAGAATTTGTACGCAGAATCTTCACCAACCCAGTAAGAATTCGGGACCCTCGGAGCCCCACAGTGGCTTCCACCTC
ACTCCTTGGCAATGGACTGAAGGCTTCAACCAAACTTTAGCTGGTTGATGCCATGGTGGACAGGCTTGCCATAGGTGGCA
CCTTAGGAAATGGGGTTTGCGGCCACCATGGCACACACAAATCTGATACATGGCAAAACCTTGCTTGGCCTTGTATCCCA
GTCTGCTCACCTTATCGGGCCAGGTGGAGCGGGGGCCCTGTGGAGAGCGGAGAGCTATCAGTACTGCCGGCAGCGCACCC
GCACCCAGAGGAGAAAGCACATTGACGTTGGATGCTTCTTCCTCCA
ORF - retro_sscr_970 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.83 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | FYKHYLLAVTVELESIAPSPSCTAGTTNSVVELVALSKAAALSACRSQPSHLPMLVDWFGDPLGVRISSD |
| FYK..LLAVTVELESI.PSPSC.A.TTNSVVELVA..KA.A.S.CRSQPS.LP.LVDW.GDPLGVRISSD | |
| Retrocopy | FYKLDLLAVTVELESIEPSPSCRASTTNSVVELVAQPKAVAPSTCRSQPSPLPVLVDWSGDPLGVRISSD |
| Parental | SFMEWINEDNLKEFVCRIFTNPVRIQDSQSPTVASSSLLGGKNGPSCDLELVDTMVDRLAVGGT-LRNW- |
| SFMEWINEDNLKEFV.RIFTNPVRI.D..SPTVAS.SLLG.....S..L.LVD.MVDRLA.GGT.LR.W. | |
| Retrocopy | SFMEWINEDNLKEFVRRIFTNPVRIRDPRSPTVASTSLLGNGLKASTKL*LVDAMVDRLAIGGT<LRKW< |
| Parental | AFAATAAHTNPIYDITGRTLTLLGLVSQPARLIGPGGA-GGPVESGELAVLPAA--HPEEKAHDVGLLLP |
| .FAAT.AHTN.I....G.T..LLGLVSQ.A.LIGPGGA.GGPVESGEL.VLPAA..HPEEKAH....LLP | |
| Retrocopy | GFAATMAHTNLIH---GKT--LLGLVSQSAHLIGPGGA<GGPVESGELSVLPAAHPHPEEKAH*RWMLLP |
| Parental | P |
| P | |
| Retrocopy | P |
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 .00 RPM |
| SRP014902_testis | 0 .00 RPM | 0 .00 RPM |
| SRP018288_heart | 0 .00 RPM | 0 .21 RPM |
| SRP018288_kidney | 0 .00 RPM | 0 .30 RPM |
| SRP018288_liver | 0 .00 RPM | 0 .00 RPM |
| SRP018288_lung | 0 .00 RPM | 0 .00 RPM |
| SRP018856_adipose | 0 .00 RPM | 0 .00 RPM |
| SRP035408_brain | 0 .00 RPM | 0 .03 RPM |
| SRP035408_liver | 0 .00 RPM | 0 .00 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_970 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_970 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_970 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000030310 | 2 retrocopies |
retro_sscr_970 , retro_sscr_994,
|