RetrogeneDB ID: | retro_pabe_853 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:63053358..63053674(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM242 | ||
| Ensembl ID: | ENSPPYG00000017271 | ||
| Aliases: | None | ||
| Description: | Transmembrane protein 242 [Source:UniProtKB/Swiss-Prot;Acc:Q5R987] |
Retrocopy-Parental alignment summary:
>retro_pabe_853
GGCTCTGGGACTGGGCAGCTGGCCTCTCTGCTGGAGGCTTCGGGGTCCACGGATGACTGGCTTTTCCTGGTTAAAGGTGG
AATTTTCCTTGGTATTGTTGCTGCAGCAGGAATGCTAGCTGGATTTATTACAACATTATCATTGGCTAAAAAGAAAAGCC
CTGAATGGTTCAATAAGGGAAGTACGGCCACCATCGCATTACCGGAAAGCGGGTCTTCCCTTGCCTTACTGAGCTCTGGG
CTGGGGCTTACTGTATGCATGGTATGGGGTTGGTGTGATTAGCTTCTCAGTCGGGAAAGCTTTAGGAGTTCACAGT
ORF - retro_pabe_853 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.85 % |
| Parental protein coverage: | 74.47 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GAGTGQPASGLEAPGSADDRLFLVKGGIFLGTVAAAGMLAGFITTLSLAKKKSPEWFNKGSMATAALPES |
| G.GTGQ.AS.LEA.GS.DD.LFLVKGGIFLG.VAAAGMLAGFITTLSLAKKKSPEWFNKGS.AT.ALPES | |
| Retrocopy | GSGTGQLASLLEASGSTDDWLFLVKGGIFLGIVAAAGMLAGFITTLSLAKKKSPEWFNKGSTATIALPES |
| Parental | GSSLALR-ALGWGSLYAWCGVGVISFAVWKALGVHS |
| GSSLAL..ALGWG.LYAW.GVGVISF.V.KALGVHS | |
| Retrocopy | GSSLALL>ALGWGLLYAWYGVGVISFSVGKALGVHS |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 28 .03 RPM |
| SRP007412_cerebellum | 0 .12 RPM | 36 .60 RPM |
| SRP007412_heart | 0 .00 RPM | 12 .97 RPM |
| SRP007412_kidney | 0 .00 RPM | 16 .51 RPM |
| SRP007412_liver | 0 .00 RPM | 11 .81 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_853 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_853 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_853 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1016 |
| Pan troglodytes | retro_ptro_747 |
| Macaca mulatta | retro_mmul_812 |
Parental genes homology:
Parental genes homology involve 9 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000009699 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000022213 | 1 retrocopy | |
| Equus caballus | ENSECAG00000016335 | 1 retrocopy | |
| Homo sapiens | ENSG00000215712 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000011814 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000010676 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000007646 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017271 | 1 retrocopy |
retro_pabe_853 ,
|
| Pan troglodytes | ENSPTRG00000018735 | 1 retrocopy |