RetrogeneDB ID: | retro_sscr_1167 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | X:79962513..79963067(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000030794 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KLHL7 | ||
| Ensembl ID: | ENSSSCG00000024897 | ||
| Aliases: | None | ||
| Description: | kelch-like family member 7 [Source:HGNC Symbol;Acc:15646] |
Retrocopy-Parental alignment summary:
>retro_sscr_1167
CTATTTGGAATCTTCCAACCACAGTCTTGTAGATATTTTAACCCAAAGGATTATAGCTGGACAGACATCCACTGCCCCTT
TGAAAAACGAAGAGATGCAGCATGCATGTTTGGGGACAATGTAGTTTACATTTTGGGTGGCTCTCAGCTTTTCCCCATAA
AATGAATGGACTGTTAAAATGTCGTAAAGGATAGGTGGTTTTCCAAACTGGGTCCTCCAACACCTCAAGACAGCCTTGCT
GCCTGTGCTGCAGAAGGGAAAATTTATACCTCTGGAGGTTCCAAAGTCGGAAACTCAGCTCTGTATTTATTTGAGTGCTA
CAACATGAGAAATGAAAGCTGGCACACAAAGCCCAACATGCCGACTAAGCGCTGCAACCATCGACGGTGGAAACCAATGG
CCTGCTTTATATTTGTGGTGGAAGTTTAGGGAACAACGTTTCTGAGCGAGTATTGAAATTGTGTGAATTCTATGATCCTG
CCACAGAAAAATGGACTGAGCTGTGTCCAATGATTGAAGCCAGGAAGAATCATGGACCGGTATTTGTAAAAGAC
ORF - retro_sscr_1167 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.49 % |
| Parental protein coverage: | 63.79 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LFKFSITESFHPFLLQDYSWTDIRCPFEKRRDAACVFWDNVVYILGGSQLFPIKRMDCYNVVKDSWYSKL |
| LF......S...F...DYSWTDI.CPFEKRRDAAC.F.DNVVYILGGSQLFPIK.MDC.NVVKD.W.SKL | |
| Retrocopy | LFGIFQPQSCRYFNPKDYSWTDIHCPFEKRRDAACMFGDNVVYILGGSQLFPIK*MDC*NVVKDRWFSKL |
| Parental | GPPTPRDSLAACAAEGKIYTSGGSEVGNSALYLFECYDTRTESWHTKPSMLTQRCSH-GMVEANGLIYVC |
| GPPTP.DSLAACAAEGKIYTSGGS.VGNSALYLFECY..R.ESWHTKP.M.T.RC.H...VE.NGL.Y.C | |
| Retrocopy | GPPTPQDSLAACAAEGKIYTSGGSKVGNSALYLFECYNMRNESWHTKPNMPTKRCNH<STVETNGLLYIC |
| Parental | GGSLGNNVSGRVLNSCEVYDPATETWTELCPMIEARKNHGLVFVKD |
| GGSLGNNVS.RVL..CE.YDPATE.WTELCPMIEARKNHG.VFVKD | |
| Retrocopy | GGSLGNNVSERVLKLCEFYDPATEKWTELCPMIEARKNHGPVFVKD |
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 | 1 .73 RPM |
| SRP014902_testis | 0 .14 RPM | 13 .15 RPM |
| SRP018288_heart | 0 .05 RPM | 7 .18 RPM |
| SRP018288_kidney | 0 .89 RPM | 15 .47 RPM |
| SRP018288_liver | 0 .16 RPM | 7 .52 RPM |
| SRP018288_lung | 0 .00 RPM | 8 .04 RPM |
| SRP018856_adipose | 0 .15 RPM | 10 .25 RPM |
| SRP035408_brain | 0 .44 RPM | 21 .34 RPM |
| SRP035408_liver | 0 .09 RPM | 2 .00 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1167 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1167 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1167 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000024897 | 1 retrocopy |
retro_sscr_1167 ,
|
| Sus scrofa | ENSSSCG00000026353 | 1 retrocopy |