RetrogeneDB ID: | retro_mdom_1277 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:252483612..252484074(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C1orf131 | ||
| Ensembl ID: | ENSMODG00000009357 | ||
| Aliases: | None | ||
| Description: | chromosome 1 open reading frame 131 [Source:HGNC Symbol;Acc:25332] |
Retrocopy-Parental alignment summary:
>retro_mdom_1277
CTAATACCTCCCAAGAATGAGGATGCAAAAACCAAAGTCAAGATCCCTTAGAAGGGATCAGATATGCAAAAATTTAATTT
GGAAAAGGCTCATTTGGAAGTGCATCAACTTAGGATCATTGGATAGGAAGGGGAAAGAATGGATTCTTGAATGGGAGATA
GCATTCATCCTGTGTGTCATGTCCTCCCCCAAAAAATATTGCATTAATTACAAAGTTTCGTAGAAGCAGATGGGGGGAGG
GGAGCAGCAAAAGAAGAAGAAAATAGAGTGGCTACGGTTAGAGACTTTCAGAAAAGAAAGAATAGAAAAGGTTCAGAGAA
TCATTAGAAGTCCAAAAAGAAGAAATCAGCTCCCAGTATTTTGTCAACAACATCAATAGGGCAAATTGAAAAATTCAAAA
TTGGGACACTGATTCCTAGTAGTATGGATATCAAGAAAATAAATTCATTCAAAGAAATTAAA
ORF - retro_mdom_1277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.39 % |
| Parental protein coverage: | 52.92 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LEPPKDEDTKTKANIPEKESDMQEFNLEKARLEVHRFGITG-YGKG-KERILEQERAIMLGA-KPPKNNY |
| L.PPK.ED.KTK..IP.K.SDMQ.FNLEKA.LEVH...I.G..G.G.KE.ILE.E.A..L.....PK... | |
| Retrocopy | LIPPKNEDAKTKVKIP*KGSDMQKFNLEKAHLEVHQLRIIG<IGRG<KEWILEWEIAFILCVMSSPKKYC |
| Parental | VNYKVLQEQI-KGKKAAMEEEKRMAQITDAFRKKKRKGSEDSRKSKKKKSAPSILSTGSAGQIGKFKNGT |
| .NYKV...Q...G..AA.EEE.R.A...D....K.RKGSE...KSKKKKSAPSILST.S.GQI.KFK.GT | |
| Retrocopy | INYKVS*KQM<GGRGAAKEEENRVATVRDFQKRKNRKGSENH*KSKKKKSAPSILSTTSIGQIEKFKIGT |
| Parental | LILSSVDIKKINSSKGIK |
| LI.SS.DIKKINS.K.IK | |
| Retrocopy | LIPSSMDIKKINSFKEIK |
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_1277 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1277 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000009357 | 1 retrocopy |
retro_mdom_1277 ,
|
| Oryctolagus cuniculus | ENSOCUG00000005657 | 1 retrocopy |