RetrogeneDB ID: | retro_sscr_561 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 17:2598556..2598761(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SNRPD2 | ||
| Ensembl ID: | ENSSSCG00000025813 | ||
| Aliases: | None | ||
| Description: | small nuclear ribonucleoprotein D2 polypeptide 16.5kDa [Source:HGNC Symbol;Acc:11159] |
Retrocopy-Parental alignment summary:
>retro_sscr_561
AGCCTCCTCAACAAGCCCAAGGGTAAGATGACCCCAGGGGGGGCTGTAGAAGTTGGGGGAGGAGGAGTTTAACACGGGTC
CACTGTCCATGCTCAAGCAGTCAGTCAAGAACAACACCCAAGTGCTTATCAACTGCCACAACAAGAAGCTCCTGGGCCAC
GTGAAGGCCTTTGACAGACACTGCAACATGGTCCTGGAGAATGTG
ORF - retro_sscr_561 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.43 % |
| Parental protein coverage: | 66.35 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SLLNKPKSEMTPEE-LQKREEEEFNTGPLSVLTQSVKNSRKGSVNVTHGHQALGGFQGFSRHCNMVLENV |
| SLLNKPK..MTP...L.K..EEEFNTGPLS.L.QSVKN......N..H....LG....F.RHCNMVLENV | |
| Retrocopy | SLLNKPKGKMTPGG>L*KLGEEEFNTGPLSMLKQSVKNNTQVLIN-CHNKKLLGHVKAFDRHCNMVLENV |
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 | 70 .75 RPM |
| SRP014902_testis | 0 .14 RPM | 93 .35 RPM |
| SRP018288_heart | 0 .00 RPM | 30 .36 RPM |
| SRP018288_kidney | 0 .00 RPM | 37 .14 RPM |
| SRP018288_liver | 0 .00 RPM | 26 .39 RPM |
| SRP018288_lung | 0 .00 RPM | 35 .13 RPM |
| SRP018856_adipose | 0 .00 RPM | 141 .75 RPM |
| SRP035408_brain | 0 .00 RPM | 47 .58 RPM |
| SRP035408_liver | 0 .00 RPM | 27 .45 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_561 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_561 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_561 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 | ENSSSCG00000025813 | 1 retrocopy |
retro_sscr_561 ,
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