RetrogeneDB ID: | retro_sscr_174 | ||
Retrocopylocation | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 1:124839674..124839946(-) | ||
| Located in intron of: | ENSSSCG00000004587 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | CXCL2 | ||
| Ensembl ID: | ENSSSCG00000008959 | ||
| Aliases: | CXCL2, GRO2, GROB, MIP2, MIP2A, SCYB2 | ||
| Description: | Sus scrofa chemokine (C-X-C motif) ligand 2 (CXCL2), mRNA. [Source:RefSeq mRNA;Acc:NM_001001861] |
Retrocopy-Parental alignment summary:
>retro_sscr_174
CTCTGCACTGTGCTGCTGCTTCTGTTCCTGGTGACCCCAGCTGGCATGCAGCAGGGGGGCACATGGTCACGAATTGTGCT
GCCAGTGCATGCAGACCCTGCAGGGAATCCACCTCAGGAATATCCACAGAGTGAAGGTGATACGCCCCGGACTCCATTGT
GGCTAAAGAGAAGTCATAGACACTTTCCAGGCTGATAAGAAAGTGTGTCTCAACCTGCACCCCCCTGGTTAAGAAAATCA
CTGAGAAGATGCTAAACAAGAGCAGTGCTGAC
CTCTGCACTGTGCTGCTGCTTCTGTTCCTGGTGACCCCAGCTGGCATGCAGCAGGGGGGCACATGGTCACGAATTGTGCT
GCCAGTGCATGCAGACCCTGCAGGGAATCCACCTCAGGAATATCCACAGAGTGAAGGTGATACGCCCCGGACTCCATTGT
GGCTAAAGAGAAGTCATAGACACTTTCCAGGCTGATAAGAAAGTGTGTCTCAACCTGCACCCCCCTGGTTAAGAAAATCA
CTGAGAAGATGCTAAACAAGAGCAGTGCTGAC
ORF - retro_sscr_174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.29 % |
| Parental protein coverage: | 85.98 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LRAALLLLLLVAAGR-RAAGAPV-GGELRCQCLQTVQGIHLKNIQDLKVTSPGPHCDQTEVIATLKNGQE |
| L...LLLL.LV......AAG....G.EL.CQC.QT.QGIHL.NI...KV..PG.HC...EVI.T...... | |
| Retrocopy | LCTVLLLLFLVTPAG<HAAGGHM<GHELCCQCMQTLQGIHLRNIHRVKVIRPGLHCG*REVIDTFQADKK |
| Parental | VCLN-PA-APMVKKIIEKMLNKSSAN |
| VCLN.PA..P.VKKI.EKMLNKSSA. | |
| Retrocopy | VCLN<PA<TPLVKKITEKMLNKSSAD |
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 .13 RPM | 1 .33 RPM |
| SRP014902_testis | 0 .00 RPM | 1 .41 RPM |
| SRP018288_heart | 0 .00 RPM | 2 .36 RPM |
| SRP018288_kidney | 0 .00 RPM | 0 .49 RPM |
| SRP018288_liver | 0 .00 RPM | 0 .32 RPM |
| SRP018288_lung | 0 .00 RPM | 12 .32 RPM |
| SRP018856_adipose | 0 .00 RPM | 8 .07 RPM |
| SRP035408_brain | 0 .00 RPM | 0 .00 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_174 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_174 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_174 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000008959 | 1 retrocopy |
retro_sscr_174 ,
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