RetrogeneDB ID: | retro_sscr_1166 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | X:79961810..79962408(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000030794 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000026353 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_1166
ACTTAAAAAATGCTTGAATCAAAGTCCTTTGAAGTAGAACTCAAAGATGCTGAACCTGACATTATTGAACAATTTGTGGA
ATTTGCTTATACTGCTAGAATTTCTGTGAATAGCAACAATGTTCAGTCTCTGTTAGATGCAGCAAATCAGCACCAGATTG
AACTGTGAAGAAAATGTGTGTTGATTTTTTGAAAGAACAAGTCAATGTTTCAAATTGTCTTGGTATAAGTGTGCCAGCAG
AGTGTCTAGACTGTCCTGAATTGAAGGTAACTGCAGATGACTTCATTCATCAACATTTTAATGAAGTTTATAAAACTGAT
GAATTTCTGCAGCTTGATGCCAAGCGAGTCACGCATCTCAACCAGGACACTTTGACTATGAAAGCAGATCAGGTTTATGA
TGATGCAGTCAGGTTGTTGAAATATGATGAACCTAATCACCAGCCATTTATGGTTGACATCATACTAAAGTCAGATTTCC
TCTTATATCAAAGAATTTCTTAAGCAAAACAGTACAAGCTGAACCACTTATTCAAGACAATCCTGAATTCCTTAAGATGG
TGATAAGTGGAATGAGGTATCATCTTCTGTCTCCTGAG
ORF - retro_sscr_1166 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.73 % |
| Parental protein coverage: | 93.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TTNMLESKSFEVELKDAEPDIIEQLVEFAYTARISVNSNNVQSLLDAANQYQIE-PVKKMCVDFLKEQVD |
| T..MLESKSFEVELKDAEPDIIEQ.VEFAYTARISVNSNNVQSLLDAANQ.QIE..VKKMCVDFLKEQV. | |
| Retrocopy | T*KMLESKSFEVELKDAEPDIIEQFVEFAYTARISVNSNNVQSLLDAANQHQIE<TVKKMCVDFLKEQVN |
| Parental | ASNCLGISVLAECLDCPELKATADDFIHQHFTEVYKTDEFLQLDVKRVTHLLNQDTLTVRAEDQVYDAAV |
| .SNCLGISV.AECLDCPELK.TADDFIHQHF.EVYKTDEFLQLD.KRVTH.LNQDTLT..A.DQVYD.AV | |
| Retrocopy | VSNCLGISVPAECLDCPELKVTADDFIHQHFNEVYKTDEFLQLDAKRVTH-LNQDTLTMKA-DQVYDDAV |
| Parental | RWLKYDEPNRQPFMVDIL-AKVRFPLISKNFLSKTVQAEPLIQDNPECLKMVISGMRYHLLSPE |
| R.LKYDEPN.QPFMVDI...KVRFPLISKNFLSKTVQAEPLIQDNPE.LKMVISGMRYHLLSPE | |
| Retrocopy | RLLKYDEPNHQPFMVDII<TKVRFPLISKNFLSKTVQAEPLIQDNPEFLKMVISGMRYHLLSPE |
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 | 0 .40 RPM |
| SRP014902_testis | 0 .28 RPM | 2 .26 RPM |
| SRP018288_heart | 0 .03 RPM | 3 .72 RPM |
| SRP018288_kidney | 0 .20 RPM | 6 .40 RPM |
| SRP018288_liver | 0 .16 RPM | 3 .84 RPM |
| SRP018288_lung | 0 .10 RPM | 3 .97 RPM |
| SRP018856_adipose | 0 .00 RPM | 1 .89 RPM |
| SRP035408_brain | 1 .84 RPM | 4 .57 RPM |
| SRP035408_liver | 0 .41 RPM | 0 .70 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1166 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1166 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1166 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 | |
| Sus scrofa | ENSSSCG00000026353 | 1 retrocopy |
retro_sscr_1166 ,
|