RetrogeneDB ID: | retro_sscr_761 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 4:103785619..103786311(+) | ||
| Located in intron of: | ENSSSCG00000006542 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000017955 | ||
| Aliases: | None | ||
| Description: | Sus scrofa mannose-P-dolichol utilization defect 1 (LOC733696), mRNA. [Source:RefSeq mRNA;Acc:NM_001044619] |
Retrocopy-Parental alignment summary:
>retro_sscr_761
CTTTTACCTGAGAAATGCTATGACTGAATTTTCATCCACTGGGACTTGCTTCACGAAGTTCCTTGCCTCCGGATTCTCCT
GAGCCAGTGCCTGGGGTTGGCCATTGTAGCTGGCTCACTTCTGGAAAAACCGCCCCAAGTGTTTAAAATCCTGGGAGCCA
AGAGCGGGAAGGGTTGTGTCTACCGTCGGTGATGCTGGAGCTGGTGGCAATGACCCGGACCTTGGTCTGCAGCATCACCA
ACAACTTCCCCTTCAGCTCTTGGGGACAAGCCCTGTTCCTGATGCTCCAGAGAGTCACCATCACCCTCCTGGTCCTGCAC
TTGAGAGGACAGACTGTGAAAGGTGGGGCTTTCCTAGCGTGCTATGCTCTGGTCCTCCTGATGCTGCTTCCACCACTGAC
GCCCCTGGCTGTAGAGACCCCGCTCCAGGCCTCCAACACACCTGCTGTGGTGATGGGAAGGCTGATTCAAGCAGCCACCG
AAGACCAGAACAGGCGTACAGGCCAGCACGGAGCCATCGCAGTCTTTCTGCTCTTTGGGGGCTCCCTGGCCCGAGTCTTC
ACCTCCATTCATGAAACCGGAGACCCCCTCACGGCTGGAACCTTTGCAGTCTCTCCCCTCTGCAGCGGCCTCGTTGCTGC
CCAGCTCCTCTTCTGCTGGAATGCAAAGGCTCCCCTCAAGAAGAAGAAGGAG
ORF - retro_sscr_761 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.45 % |
| Parental protein coverage: | 93.12 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LLPEKCYDQIFVQWDLLH-VPCLKILLSKCLGLGIVAGSLLVKLPQVFKILGAKSA-EGLSLQSVMLELV |
| LLPEKCYD.IF..WDLLH.VPCL.ILLS.CLGL.IVAGSLL.K.PQVFKILGAKS..EGL.L.SVMLELV | |
| Retrocopy | LLPEKCYD*IFIHWDLLHEVPCLRILLSQCLGLAIVAGSLLEKPPQVFKILGAKSG<EGLCLPSVMLELV |
| Parental | ALTGTMVYSITNNFPFSSWGEALFLMLQTVTIAFLVLHYRGQTVRGVAFLACYAVLLLMLLSPLTPLALV |
| A.T.T.V.SITNNFPFSSWG.ALFLMLQ.VTI..LVLH.RGQTV.G.AFLACYA..LLMLL.PLTPLA.. | |
| Retrocopy | AMTRTLVCSITNNFPFSSWGQALFLMLQRVTITLLVLHLRGQTVKGGAFLACYALVLLMLLPPLTPLAVE |
| Parental | TLLQASNVPAVVVGRLIQAATNYRNGHTGQLSAITVFLLFGGSLARIFTSIQETGDPLLAGTFVVSSLCN |
| T.LQASN.PAVV.GRLIQAAT...N..TGQ..AI.VFLLFGGSLAR.FTSI.ETGDPL.AGTF.VS.LC. | |
| Retrocopy | TPLQASNTPAVVMGRLIQAATEDQNRRTGQHGAIAVFLLFGGSLARVFTSIHETGDPLTAGTFAVSPLCS |
| Parental | GLIAAQLLFYWNAKPPHKKKKE |
| GL.AAQLLF.WNAK.P.KKKKE | |
| Retrocopy | GLVAAQLLFCWNAKAPLKKKKE |
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 | 4 .11 RPM |
| SRP014902_testis | 0 .00 RPM | 2 .12 RPM |
| SRP018288_heart | 0 .00 RPM | 5 .42 RPM |
| SRP018288_kidney | 0 .00 RPM | 26 .01 RPM |
| SRP018288_liver | 0 .00 RPM | 15 .83 RPM |
| SRP018288_lung | 0 .00 RPM | 15 .58 RPM |
| SRP018856_adipose | 0 .05 RPM | 3 .41 RPM |
| SRP035408_brain | 0 .00 RPM | 4 .26 RPM |
| SRP035408_liver | 0 .00 RPM | 4 .93 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_761 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_761 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_761 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000018609 | 3 retrocopies | |
| Sus scrofa | ENSSSCG00000017955 | 1 retrocopy |
retro_sscr_761 ,
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