RetrogeneDB ID: | retro_sscr_992 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 8:49537021..49537313(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CDK2AP1 | ||
| Ensembl ID: | ENSSSCG00000009775 | ||
| Aliases: | None | ||
| Description: | cyclin-dependent kinase 2 associated protein 1 [Source:HGNC Symbol;Acc:14002] |
Retrocopy-Parental alignment summary:
>retro_sscr_992
TCTGGGAGTGTCCGTTCTTCTTCCACCAGTATGGTGATGTCCTCACAATACTGCCAGCGGCTGAGTGACTATGGGCCACT
GTCTCTAGGCTACACCCAGGGGAGCAGGAATAGCCAGGTGCCCCACTGTAAGTTTGCTGAGCTGCTGGCCATCATCCAAG
AGCTGGGGAAAGAGATCAGACTCATCTATGCTGGCAGCAAGAGAACGATGGAGAGACTAAAATGAGGCATCATCCTCCCT
AGAGGATTGGTGTGGGGAGTGGTGGGCTGAAACCAAATGGAATGCCAGGTCC
ORF - retro_sscr_992 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.43 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AGSVHPPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRPTYAGSKSAM |
| .GSV...STSM..SSQY.Q.LSDYGP.SLGYTQG..NSQVP..K.AELLAII.ELGKEIR..YAGSK..M | |
| Retrocopy | SGSVRSSSTSMVMSSQYCQRLSDYGPLSLGYTQGSRNSQVPHCKFAELLAIIQELGKEIRLIYAGSKRTM |
| Parental | ERLKRGIIHARGLV-RECLAETERNARS |
| ERLK.GII..RGLV..E..AET..NARS | |
| Retrocopy | ERLK*GIILPRGLV>GEWWAETKWNARS |
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 | 10 .09 RPM |
| SRP014902_testis | 0 .00 RPM | 42 .15 RPM |
| SRP018288_heart | 0 .00 RPM | 26 .32 RPM |
| SRP018288_kidney | 0 .00 RPM | 9 .06 RPM |
| SRP018288_liver | 0 .00 RPM | 4 .64 RPM |
| SRP018288_lung | 0 .00 RPM | 6 .21 RPM |
| SRP018856_adipose | 0 .00 RPM | 22 .62 RPM |
| SRP035408_brain | 0 .00 RPM | 32 .27 RPM |
| SRP035408_liver | 0 .00 RPM | 7 .98 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_992 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_992 was not experimentally validated.