RetrogeneDB ID: | retro_mdom_1285 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:291540268..291540943(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ENDOU | ||
| Ensembl ID: | ENSMODG00000009733 | ||
| Aliases: | None | ||
| Description: | endonuclease, polyU-specific [Source:HGNC Symbol;Acc:14369] |
Retrocopy-Parental alignment summary:
>retro_mdom_1285
CTCTACAGCTATGTAAATGAAGACCTTTTCTCCAAACCAACCTATGGTGCATTCATCAGTCTACTCAATAACTACCACCA
GGTAACAGGTCAGGGGGAACACTTCAGTTCTCAGCAGCTTGAAGAACAAGACGCTTTTCTTCAAGAGATAATGAAGACAG
CGGTCATGAAGGAACTCTATGGCTTCCTCCATCAAAAAAACAGATACAGCTCAGAGCAATAATTTGTCAGTGACCTGAAG
AAGCTGTGGTTTGGGTTGTATTCCTGGGGCCATGATGAAGGTGACTCCAGTGGCTTTAAACATGTTTTCTCCAGTGAAGT
GAAAAAGGGAAAAGTGTCAGGATTCCATAACTGGATCTGCTTCTACTTGCAGGAGAAGGAGGGTCTGGTCAACTATTATA
GCCATAACTATGATGGGCTTTGAGACTCATATTCTGATGTTCTAGGAAGGTAATTCAACTGGGATGGCTACTTCAAAGAA
GTGGGATTGGCCTTCATTGGCAGTAGTCTGGAGTTTGCTTTCTATTCCTTGTGCTTCATCAGCTGGCCTGGTGGTGTGGG
TCATTTGAGCCTAGGTGGGTACCCCCTGGCTATCCAAGCCTATACCTGGGACAAGGTGACCTATGGAAATGGCAAGAAGT
ACATTGCTACAGCCTTTATAGTATCTTCTATGAAT
ORF - retro_mdom_1285 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.67 % |
| Parental protein coverage: | 55.5 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LYSYVNEELFSKPTYAAFISLLNNYHRVTGQGEHFSSQQLEEQDTFLREIMKTAVMKELYGFLHQKNRYS |
| LYSYVNE.LFSKPTY.AFISLLNNYH.VTGQGEHFSSQQLEEQD.FL.EIMKTAVMKELYGFLHQKNRYS | |
| Retrocopy | LYSYVNEDLFSKPTYGAFISLLNNYHQVTGQGEHFSSQQLEEQDAFLQEIMKTAVMKELYGFLHQKNRYS |
| Parental | SEQEFVSDLKKMWFGLYSRGHDEGDSSGFEHVFSGEVKKGKVSGFHNWIRFYLQEKEGLVDYYSHNYDGP |
| SEQ.FVSDLKK.WFGLYS.GHDEGDSSGF.HVFS.EVKKGKVSGFHNWI.FYLQEKEGLV.YYSHNYDG. | |
| Retrocopy | SEQ*FVSDLKKLWFGLYSWGHDEGDSSGFKHVFSSEVKKGKVSGFHNWICFYLQEKEGLVNYYSHNYDGL |
| Parental | WDSYPDVLGMQFNWDGYFKEVGSAFIGSSPEFEFALYSLCFISRPGGVCHLSLGGYPLAIKTYTWDKVTY |
| .DSY.DVLG..FNWDGYFKEVG.AFIGSS...EFA.YSLCFIS.PGGV.HLSLGGYPLAI..YTWDKVTY | |
| Retrocopy | *DSYSDVLGR*FNWDGYFKEVGLAFIGSS--LEFAFYSLCFISWPGGVGHLSLGGYPLAIQAYTWDKVTY |
| Parental | GNGKKYIATAYIVSSTN |
| GNGKKYIATA.IVSS.N | |
| Retrocopy | GNGKKYIATAFIVSSMN |
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_1285 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1285 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 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000009733 | 2 retrocopies |
retro_mdom_1285 , retro_mdom_962,
|