RetrogeneDB ID: | retro_mdom_1993 | ||
Retrocopylocation | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | X:22407890..22408281(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSMODG00000002960 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | RAB5A | ||
| Ensembl ID: | ENSMODG00000014793 | ||
| Aliases: | None | ||
| Description: | RAB5A, member RAS oncogene family [Source:HGNC Symbol;Acc:9783] |
Retrocopy-Parental alignment summary:
>retro_mdom_1993
GAATCCGCCATTGGAAAAGCAAGTCTTGTGCTTTGATTTGTGAAGGGCCAATTTCAGGAATTTCAAGCGAGAACCATTGG
GGCGGCTTTTCTAACCCAGATTATGTGTTTTGATGACACAGCGGTGAAATTTGAAATATGGGATACAGCTGTACAAGAAC
GATATCATAGCTTAGCACCGATGTACGCCAGAGTTGCACAAGCAGCAATAGTTGTATATGATATCACAAATGAGGAGTCC
TTTGCAAGAGCAAAAAACTGGGTCAAAGAAGCAGAGGCAAGCAAGTCCTAACATTGTAATAGCTTTAGCAGGGAACAAGG
CTGATCTAGCAAGGAAAAGAACTGTAGATTTCCAGGAAGCACAGTCTTATGCAGATGACAAGTTTATTATT
GAATCCGCCATTGGAAAAGCAAGTCTTGTGCTTTGATTTGTGAAGGGCCAATTTCAGGAATTTCAAGCGAGAACCATTGG
GGCGGCTTTTCTAACCCAGATTATGTGTTTTGATGACACAGCGGTGAAATTTGAAATATGGGATACAGCTGTACAAGAAC
GATATCATAGCTTAGCACCGATGTACGCCAGAGTTGCACAAGCAGCAATAGTTGTATATGATATCACAAATGAGGAGTCC
TTTGCAAGAGCAAAAAACTGGGTCAAAGAAGCAGAGGCAAGCAAGTCCTAACATTGTAATAGCTTTAGCAGGGAACAAGG
CTGATCTAGCAAGGAAAAGAACTGTAGATTTCCAGGAAGCACAGTCTTATGCAGATGACAAGTTTATTATT
ORF - retro_mdom_1993 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.45 % |
| Parental protein coverage: | 60.93 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAI |
| ESA.GK.SLVL.FVKGQF.EFQ..TIGAAFLTQ..C.DDT.VKFEIWDTA.QERYHSLAPMY.R.AQ.A. | |
| Retrocopy | ESAIGKASLVL*FVKGQFQEFQARTIGAAFLTQIMCFDDTAVKFEIWDTAVQERYHSLAPMYARVAQ-AA |
| Parental | VV-YDITNEESFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVDFQEAQSYADDNSLL |
| .V.Y.I....S...........QRQASPNIVIALAGNKADLA.KR.VDFQEAQSYADD.... | |
| Retrocopy | IV>YMISQMRSPLQEQKTGSKKQRQASPNIVIALAGNKADLARKRTVDFQEAQSYADDKFII |
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 .00 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1993 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1993 was not experimentally validated.