RetrogeneDB ID: | retro_acar_103 | ||
Retrocopy location | Organism: | Anole lizard (Anolis carolinensis) | |
| Coordinates: | 3:194924345..194924681(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PIGF | ||
| Ensembl ID: | ENSACAG00000028483 | ||
| Aliases: | None | ||
| Description: | phosphatidylinositol glycan anchor biosynthesis, class F [Source:HGNC Symbol;Acc:8962] |
Retrocopy-Parental alignment summary:
>retro_acar_103
TCAGTCTTAGAGACCTTTTTATTTGCTGTTTTTCTGTCCACCTTTACTACTTTGCACTGCTTGTGTTTGCTGGGACCAAA
CATTCACGTATGGCTCAGAGTGTTCAGTAAAAATGTGGCTATGTCAAGCTGGTATAACAACCTTCAGATTGCCAGTATGT
GCAGTGTGGTGGGTGCATGGCTTGGAGATTTTCCTATTCCATTGGATTGGGATAGACCATGTTAGGTTTGACCCAACTCT
CGTTCGCTCGGAGCCACTTTGGGCTATGTGTCCGGTCTTCTTTTTGCACCCTTATGGATATACTGGAACAGGATGAAGCT
TACATACAAAAGCAAA
ORF - retro_acar_103 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.39 % |
| Parental protein coverage: | 51.14 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SVLETFLFAVLLSTFTTLHCLCLLGPNIHVWLRVFSKNGAMSIWDNNLQITSMCSVVGAWLGAFPIPLDW |
| SVLETFLFAV.LSTFTTLHCLCLLGPNIHVWLRVFSKN.AMS.W.NNLQI.SMCSVVGAWLG.FPIPLDW | |
| Retrocopy | SVLETFLFAVFLSTFTTLHCLCLLGPNIHVWLRVFSKNVAMSSWYNNLQIASMCSVVGAWLGDFPIPLDW |
| Parental | DRPWQVWPISCSLGATLGYVSGLLFAPLWIYWNRKKLTYKSR |
| DRP..V.P.S.SLGATLGYVSGLLFAPLWIYWNR.KLTYKS. | |
| Retrocopy | DRPC*V*PNSRSLGATLGYVSGLLFAPLWIYWNRMKLTYKSK |
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 |
|---|---|---|
| SRP009831_adrenal | 0 .00 RPM | 18 .77 RPM |
| SRP009831_brain | 0 .00 RPM | 15 .57 RPM |
| SRP009831_dewlap | 0 .04 RPM | 40 .16 RPM |
| SRP009831_embryo | 0 .00 RPM | 22 .11 RPM |
| SRP009831_heart | 0 .00 RPM | 11 .10 RPM |
| SRP009831_liver | 0 .00 RPM | 12 .31 RPM |
| SRP009831_lung | 0 .00 RPM | 6 .10 RPM |
| SRP009831_ovary | 0 .00 RPM | 39 .19 RPM |
| SRP009831_skeletal_muscle | 0 .00 RPM | 7 .07 RPM |
Anolis carolinensis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_acar_103 retrocopy.
Anolis carolinensis was not studied using FANTOM5 data.
retro_acar_103 was not experimentally validated.