RetrogeneDB ID: | retro_mdom_1643 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 6:24603890..24604178(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PCYT1A | ||
| Ensembl ID: | ENSMODG00000018432 | ||
| Aliases: | None | ||
| Description: | phosphate cytidylyltransferase 1, choline, alpha [Source:HGNC Symbol;Acc:8754] |
Retrocopy-Parental alignment summary:
>retro_mdom_1643
TGCATCCATGCCAGAATTAAGGAAGATTCGGCACCTGCTCAGTACAGAGTCAGATGATATGCCTACATTCACAAATATTT
TGCCAGAGAATATGAAAAATAAACGTAAAGAAATGGGGTTTGATTAATATCAACTGTTATGACAAGTAGTGATTGGAGAA
GAAATAGGTAGAGGAATAAGGATCGCTACTCAGTGTTTCTGGGATAGTGACACAGACAACGGCACTTACGATGTTTTTAA
GAATGACAGTTTGTTCTGTCTTGTAGCTGCCTTGGCTGTTTCTACCAT
ORF - retro_mdom_1643 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.2 % |
| Parental protein coverage: | 73.28 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | CIHTILKEELATAQY-EPSEMPALTKYLSESIKNKLKEMGFDRYKMVVQVVIGEQRGEGVNMAARCFWDA |
| CIH...KE..A.AQY.E...MP..T..L.E..KNK.KEMGFD.Y....QVVIGE..G.G...A..CFWD. | |
| Retrocopy | CIHARIKEDSAPAQY>ESDDMPTFTNILPENMKNKRKEMGFD*YQLL*QVVIGEEIGRGIRIATQCFWDS |
| Parental | DTDNYTHDVFMNDSLFCVVAA-FGCFYY |
| DTDN.T.DVF.NDSLFC.VAA..GCFY. | |
| Retrocopy | DTDNGTYDVFKNDSLFCLVAA<LGCFYH |
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_1643 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1643 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000010073 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000018432 | 1 retrocopy |
retro_mdom_1643 ,
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