RetrogeneDB ID: | retro_cpor_1321 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_7:40779703..40780223(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ST3GAL6 | ||
| Ensembl ID: | ENSCPOG00000013240 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1321
GGTAGAGAGAGATGTGACCTACCCTGGGGGCGCGCGTCCCGGGTGTGCATCCGGGGTGCGCTTTCCTGGTATTGCGCAGC
TGCGACGGCTCTGAGTATTATGCCAGTGAACCACGCACCTAAGAACGTGGTGCTTGGCAATGGAGGAGTTTCGAGGCATA
AGACATTGTGAGCAAAAATGAACTCCTAAGATGTAATAAAAAGAAGCAATGATGGTCCGGTGTTAGGTCATGAAGAGGAA
GCTGGGAGGAGGACAGCTTTCTGACTTTTTTGTCCAGAAGCTGTTTTTTCCTATCCAGGCACGAGGCTCCTAAGCCACAG
CCATGCTCACTGTTCTTAAGCCACTTGATTTAAAGTGGCTGGGGGAATTGTTAACTGGTGGCAAAATAGACGCTAATGCT
AAAGAAACCAGCCTTAAACTTGATCTATAAACCTTATCAAATAAGAATATTAGATGTTTCCATATCAGGACAGCAGCTTA
GCATCCGCTTCATTTTCCAGGTGTTTCCTAAAAATCAGAA
ORF - retro_cpor_1321 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.49 % |
| Parental protein coverage: | 53.17 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | GSNKLYLPY-GIRASEEYFQLALSKLQSCDLFDEFDNEP-CKRCVVVGNGGILKNKTLGEKIDSYDVIIR |
| G.....LP..G.R........A...L.SCD.......EP.....VV.GNGG....KTL..K..S.DVI.R | |
| Retrocopy | GRERCDLPW<GARVPGVHPGCAFLVLRSCDGSEYYASEP>APKNVVLGNGGVSRHKTL*AKMNS*DVIKR |
| Parental | MNNGPVLGHEEEVGRRTTFRLFYPESVFSDPS-HSDPN-ATAILTVFKPLDLKWLEELLTGGKINTNGFW |
| .N.GPVLGHEEE.GRRT.F.LF.PE.VFS.P..H..P..ATA.LTV.KPLDLKWL.ELLTGGKI..N... | |
| Retrocopy | SNDGPVLGHEEEAGRRTAF*LFCPEAVFSYPG<HEAPK<ATAMLTVLKPLDLKWLGELLTGGKIDANA-- |
| Parental | KKPAL-NLIYKPHQIRILDP-FIIRTAAYDLLHFPKVFPKNQ |
| K...L.NLIYKP.QIRILD..F.IRTAA...LHFP.V..K.. | |
| Retrocopy | KETSL>NLIYKPYQIRILDV<FHIRTAA*HPLHFPGVS*KSE |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 9 .72 RPM |
| SRP017611_kidney | 0 .00 RPM | 18 .42 RPM |
| SRP017611_liver | 0 .00 RPM | 12 .19 RPM |
| SRP040447_lung | 0 .00 RPM | 16 .24 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 11 .28 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1321 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1321 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000013240 | 2 retrocopies |
retro_cpor_1321 , retro_cpor_1338,
|
| Dipodomys ordii | ENSDORG00000016606 | 1 retrocopy |