RetrogeneDB ID: | retro_cfam_896 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 2:40515039..40515507(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PLCB3 | ||
| Ensembl ID: | ENSCAFG00000014542 | ||
| Aliases: | None | ||
| Description: | phospholipase C, beta 3 (phosphatidylinositol-specific) [Source:HGNC Symbol;Acc:9056] |
Retrocopy-Parental alignment summary:
>retro_cfam_896
GTGGGAGATGCCATCCCTTCGGTGATAGTTTTTGAAGGGGAACCTGGAAACAAGGTGAACCTGGCAGAGCTGTTCAAGGG
CAAAAAGGGGGTGCTGTTTGGAGTCCCTAGGTCCTTTAGCCCTGGCTGTTCCAAGACCCACCTGCCAGGATTCATGGAGC
AGGCTGAGGCTCTGAAGGCCAAGGGGGTCCAAGTGATAGCCTGTCTGAGCGTTAATGATGTCTTCGTGACTGAGGCCTGG
GGACGAGCTCACAACTCAGGAGGCAAGGTTAGGCTGTTGGCTGACCCCACTGGGGCCTTTGGGAAGGAGACAGATTTGTT
ACTGGATGATTCATTGGTATCTCTCTTTGGAAATCATCAGCTCAAGAGGTTCTCTATGGTGATAGAGAATGGCATAGTGA
AGTCCTTGAATGTGGAGCCAGATGGTACAGGCCTCACCTGCAGCCTGGCTCCCAACATCCTCTCGCGC
ORF - retro_cfam_896 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.51 % |
| Parental protein coverage: | 79.19 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VGDAIPSVTVFEGEPGNEVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFMEQAEALKAKGVQVIACLS |
| VGDAIPSV.VFEGEPGN.VNLAELFKGKKGVLFGVP..F.PGCSKTHLPGFMEQAEALKAKGVQVIACLS | |
| Retrocopy | VGDAIPSVIVFEGEPGNKVNLAELFKGKKGVLFGVPRSFSPGCSKTHLPGFMEQAEALKAKGVQVIACLS |
| Parental | VNDVFVTEAWGRAHNSGGKVRLLADPTGAFGKETDLLLDDSLVSLFGNHRLKRFSMVIENGIVKSLNVEP |
| VNDVFVTEAWGRAHNSGGKVRLLADPTGAFGKETDLLLDDSLVSLFGNH.LKRFSMVIENGIVKSLNVEP | |
| Retrocopy | VNDVFVTEAWGRAHNSGGKVRLLADPTGAFGKETDLLLDDSLVSLFGNHQLKRFSMVIENGIVKSLNVEP |
| Parental | DGTGLTCSLAPNILSQ |
| DGTGLTCSLAPNILS. | |
| Retrocopy | DGTGLTCSLAPNILSR |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .17 RPM | 96 .26 RPM |
| SRP017611_brain | 0 .08 RPM | 76 .14 RPM |
| SRP017611_kidney | 0 .07 RPM | 90 .14 RPM |
| SRP017611_liver | 0 .00 RPM | 78 .02 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_896 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_896 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_896 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000014542 | 2 retrocopies |
retro_cfam_1806, retro_cfam_896 ,
|