RetrogeneDB ID: | retro_mmul_1254 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 16:30680360..30680737(-) | ||
| Located in intron of: | ENSMMUG00000005551 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB38 | ||
| Ensembl ID: | ENSMMUG00000016006 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mmul_1254
GTGAATTGTGCACTGAAGGAGCTCCACTGGGACTCAGAGGCCTTGGCGCACCTGCAGCTGTGGAACATTGCAATGAGGAA
AGATTGGGGAAATGACAAGAACCTGTTGTCTGGAATTTATAGGTGCATTGATTGTCTTCAGTATCACCAGGCCAGCCCCA
TTTGAAGCACAGTCAAAGTGGAAAAATGATTTGGACTAAATGTTAACTCATGGCAGATCAGTTTCTGTGGTTCTGCTGGC
CAAGAAATGTGACCGCGGGAGGGTGAATGCAGAAACTGTAGCCTCAAGATAGGCCAGATCTACATGGAACATAGTTTTGT
AGGATGAGTTGAAACATCAGCAAAGGAAAATGTGAACTTGATGAAGCCTCCAGGTGC
ORF - retro_mmul_1254 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.65 % |
| Parental protein coverage: | 61.14 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | VDFALKVLHWDPETVVRLQLWDIA-GQERFGN-MTRVYYREAMGAFIVFDVTRPATFEAVAKWKNDLDSK |
| V..ALK.LHWD.E....LQLW.IA...ER.G..MTR....E..GA.IVF..TRPA.FEA..KWKNDLD.. | |
| Retrocopy | VNCALKELHWDSEALAHLQLWNIA<NEERLGK<MTRTCCLEFIGALIVFSITRPAPFEAQSKWKNDLD*M |
| Parental | LTLPNGKPVSVVLLANKCDQGK-DVLMNNGLKMDQFCKEHGFVGWFETSAKENIN-IDEASRC |
| LT...G..VSVVLLA.KCD.G......N..LK..Q...EH.FVG..ETSAKEN.N..DEASRC | |
| Retrocopy | LT--HGRSVSVVLLAKKCDRGR<GECRNCSLKIGQIYMEHSFVG*VETSAKENVN<LDEASRC |
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 | 0 .11 RPM | 0 .11 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .08 RPM | 0 .32 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .26 RPM |
| SRP007412_heart | 0 .24 RPM | 0 .35 RPM |
| SRP007412_kidney | 0 .35 RPM | 3 .17 RPM |
| SRP007412_liver | 0 .04 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .11 RPM | 0 .34 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1254 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1254 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_1254 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000016006 | 1 retrocopy |
retro_mmul_1254 ,
|
| Pongo abelii | ENSPPYG00000003752 | 1 retrocopy |