RetrogeneDB ID: | retro_sscr_1010 | ||
Retrocopylocation | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 8:112209298..112209629(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSSSCG00000027086 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TMEM41A | ||
| Ensembl ID: | ENSSSCG00000025921 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 41A [Source:HGNC Symbol;Acc:30544] |
Retrocopy-Parental alignment summary:
>retro_sscr_1010
TCCATGGGTGCCAGATGCTGCCATTTCTTTCCAGTGTTTTCGGCAAACAGCTGGTGGTCTCCTACTTTCCTGGCAAAGTG
GCCCTGCTGCAAAGGAAGGTGGAGGAGAACAGAAACAACTTGTTTTTTTTTTCTTACTGTTTTTGAGACTTTTCCCCATG
ACGCCAAACCTGTTCCTGAACCTCTTGGCCCTGATTCTGAACATCCTCATCGTTCAGGTTTTCTCAGTTCTCATCGGTTT
GATCCCGTATAATTTCATCTGTGTGCAGACAGGCTGCATCCTGTCAACCCTTACCTCTCTGGATGCTATTTTCTCCTGGG
AAACTGCCTTT
TCCATGGGTGCCAGATGCTGCCATTTCTTTCCAGTGTTTTCGGCAAACAGCTGGTGGTCTCCTACTTTCCTGGCAAAGTG
GCCCTGCTGCAAAGGAAGGTGGAGGAGAACAGAAACAACTTGTTTTTTTTTTCTTACTGTTTTTGAGACTTTTCCCCATG
ACGCCAAACCTGTTCCTGAACCTCTTGGCCCTGATTCTGAACATCCTCATCGTTCAGGTTTTCTCAGTTCTCATCGGTTT
GATCCCGTATAATTTCATCTGTGTGCAGACAGGCTGCATCCTGTCAACCCTTACCTCTCTGGATGCTATTTTCTCCTGGG
AAACTGCCTTT
ORF - retro_sscr_1010 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.95 % |
| Parental protein coverage: | 64.16 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SVGATCCYL-LSSVFGKQLVVSYFPDKVALLQRKVEENRNSL-FFFLLFLRLFP-MTPNWFLNLSAPILN |
| S.GA.CC...LSSVFGKQLVVSYFP.KVALLQRKVEENRN.L....L.....FP.MTPN.FLNL.A.ILN | |
| Retrocopy | SMGARCCHF<LSSVFGKQLVVSYFPGKVALLQRKVEENRNNL>XXXLTVFETFP>MTPNLFLNLLALILN |
| Parental | IPIVQFFFSVLIGLIPYNFICVQTGSILSTLTSLDAIFSWETAF |
| I.IVQ..FSVLIGLIPYNFICVQTG.ILSTLTSLDAIFSWETAF | |
| Retrocopy | ILIVQ-VFSVLIGLIPYNFICVQTGCILSTLTSLDAIFSWETAF |
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 | 12 .87 RPM |
| SRP014902_testis | 0 .00 RPM | 8 .63 RPM |
| SRP018288_heart | 0 .00 RPM | 4 .66 RPM |
| SRP018288_kidney | 0 .00 RPM | 13 .30 RPM |
| SRP018288_liver | 0 .00 RPM | 6 .72 RPM |
| SRP018288_lung | 0 .00 RPM | 6 .62 RPM |
| SRP018856_adipose | 0 .00 RPM | 7 .12 RPM |
| SRP035408_brain | 0 .00 RPM | 6 .64 RPM |
| SRP035408_liver | 0 .00 RPM | 5 .20 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1010 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1010 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1010 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000025921 | 2 retrocopies |
retro_sscr_1010 , retro_sscr_1011,
|