RetrogeneDB ID: | retro_sscr_667 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 2:57277744..57278139(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000023391 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_667
CTGCAGAATAGCATCCTGGACCTCATTTCCAAAATGACCAACATGGATAGCAATAATCAGGGCCCACCAGCATTGCACAG
GATTGGAACAACTGCACTGACAGTTCAGGTTTTGTCAGGTTTTGGTGGGCTCCTCACTCTACATACCTTTGCTACTTTCA
GATCATACAGGTTTTTCAAGAGAAGTCATATCTTGTTGAAATGGAACTGTTGAAACAGCTTGAGAAATTTTCAACATCTG
TAAAACTAGAAAGGAGTTAGGATAAGAAGAGTTTTACAAATACAGACTACAATTTTACGAAATGTTTGGATATGTGTTTC
CCTGTGGTTGCTAAGTCAAGATGTCTTTTAGATAGTCTTCCAATAGCTCTACCAGACATTCTGACATCAATTATC
ORF - retro_sscr_667 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.24 % |
| Parental protein coverage: | 63.35 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LQSTILGVIPNTPDPASDAQDLPPLHRIGTAALAVQVVGS-NWPKPHYTLLITGLCRFQIVQVVKEKPYP |
| LQ..IL..I.......S..Q..P.LHRIGT.AL.VQV.....W..PH.T.L....C.FQI.QV..EK.Y. | |
| Retrocopy | LQNSILDLISKMTNMDSNNQGPPALHRIGTTALTVQVLSG<FWWAPHSTYL----CYFQIIQVFQEKSY- |
| Parental | VAEVEQLDRLEEFP-NTCKTREELGELSEQFYKYAVQLVEM-LDMSVPAVAKLRRLLDSLPREALPDILT |
| ..E.E.L..LE.F..N.CKTR.ELG...E.FYKY..Q..EM.LDM..P.VAK.R.LLDSLP..ALPDILT | |
| Retrocopy | LVEMELLKQLEKFS<NICKTRKELG--*EEFYKYRLQFYEM>LDMCFPVVAKSRCLLDSLP-IALPDILT |
| Parental | SII |
| SII | |
| Retrocopy | SII |
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 | 18 .85 RPM |
| SRP014902_testis | 0 .00 RPM | 16 .83 RPM |
| SRP018288_heart | 0 .00 RPM | 12 .26 RPM |
| SRP018288_kidney | 0 .00 RPM | 24 .33 RPM |
| SRP018288_liver | 0 .00 RPM | 57 .57 RPM |
| SRP018288_lung | 0 .00 RPM | 25 .05 RPM |
| SRP018856_adipose | 0 .00 RPM | 24 .17 RPM |
| SRP035408_brain | 0 .00 RPM | 4 .80 RPM |
| SRP035408_liver | 0 .00 RPM | 26 .57 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_667 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_667 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_667 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 | ENSSSCG00000023391 | 1 retrocopy |
retro_sscr_667 ,
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