RetrogeneDB ID: | retro_cpor_1338 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_7:37045909..37046543(-) | ||
| 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_1338
AAGTGCGTAGTGTTTAGCTATGGAGGAGTTTCGAGGCATAAGACATTGTGAGCAAAAATGGACTCCTAAGATGTAATAAA
AAGAAGCAATGATGATTCGGTATTAGGTCATGAAGAGGAAGCTGGGAGGAGGGCAGCTTTCTGACTTTTTTGTCCAGAAG
CTGTGTTTTTCCTATCCATGAACGAGGCTCCTAAGCCACAGCTATGCTCACTGTTCTTAAGCCACTTGATTTAAAGTGGC
TGGGGGAATTGTTAACTGGTGGCAAAATAGACGCTAATGCTAAAGAAACCGGCCTTAAACTTGATCTATAAACCTTATCA
AACAAGAATATTATGTTTCCATATCAGGACAGCAGCTTAGCATCTGCTTCATTTTCCAGGTGTTTCCCAAAAATCAGAAA
CGCAAACACCCAACAACAGGAAATATTGCCATCACCCTTGCAATTCATACAGCTCAGGAACTTCATTTAGCTGGCTGTCA
ATACAACTTTTCTGACCTTAAGAGTCCTTCGCACTCCTGTGGGGATGCCCCCATGTCCTAGATGAACAAGAACGCTCAGC
GCAAAGGGACTGCAGAACAGCTCTTTCAAACGGACATAATGGAACAAAACTTTGTAATCAGCTTGACAGAAGAT
ORF - retro_cpor_1338 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.01 % |
| Parental protein coverage: | 64.95 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | RCVVVGNGGILKNKTLGEKIDSYDVIIRMNNGPVLGHEEEVGRRTTFRLFYPESVFSDPSHSDPN-ATAI |
| .CVV...GG....KTL..K.DS.DVI.R.N...VLGHEEE.GRR..F.LF.PE.VF.......P..ATA. | |
| Retrocopy | KCVVFSYGGVSRHKTL*AKMDS*DVIKRSNDDSVLGHEEEAGRRAAF*LFCPEAVFFLSMNEAPK<ATAM |
| Parental | LTVFKPLDLKWLEELLTGGKINTNGFWKKPALNL-IYKPHQIRILDPFIIRTAAYDLLHFPKV-FP-KNQ |
| LTV.KPLDLKWL.ELLTGGKI..N...K...L.L.IYKP.Q.RIL..F.IRTAA..LLHFP.V.FP.KNQ | |
| Retrocopy | LTVLKPLDLKWLGELLTGGKIDANA--KETGLKL>IYKPYQTRIL-CFHIRTAA*HLLHFPGV<FP<KNQ |
| Parental | KPKHPTTGMIAITLAFHICHEVHLAGFKYNLSDLKSPLHYYGNATMSLMNKNAYHNVTAEQLFLKGIIEK |
| K.KHPTTG.IAITLA.H...E.HLAG..YN.SDLKSP.H..G.A.MS.MNKNA....TAEQLF...I.E. | |
| Retrocopy | KRKHPTTGNIAITLAIHTAQELHLAGCQYNFSDLKSPSHSCGDAPMS*MNKNAQRKGTAEQLFQTDIMEQ |
| Parental | NFVINLTED |
| NFVI.LTED | |
| Retrocopy | NFVISLTED |
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_1338 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1338 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 |