RetrogeneDB ID: | retro_mdom_1310 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:402546835..402547472(+) | ||
| Located in intron of: | ENSMODG00000029397 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IMPA1 | ||
| Ensembl ID: | ENSMODG00000006271 | ||
| Aliases: | None | ||
| Description: | inositol(myo)-1(or 4)-monophosphatase 1 [Source:HGNC Symbol;Acc:6050] |
Retrocopy-Parental alignment summary:
>retro_mdom_1310
TCTCACAGTTTCATTGGTGAGGAATCAGTGGCTGCTGGGGACCACAGTGTCTTGACTGATAATCCCACATGGATAATTGA
TCCTATTGATGGAACTATTAACTTCGTGCACAGATTTCCATTTGTAGCTATTTCCATTGGCTTTGATGTGGGCAAAAAGA
TGGAATTTGGAGTTGTATACAGTTGTATAGAAGATAAAATGTACACTGGCAGGAAAGGAAAATGGACTTTTTGCAATGAT
CAAAAACTTCATGTGTCAGGACAAAAAGATTTTGCTAAAATTGGTGACAGAATTGGTAGTTAACCGACAACCAGAGGTGG
TAAAAACTTTTCTTTCAAATATGGAGATACTTTTTTATATTCCTATTCATGGAATAAGGGGTGCTGGTACAGCAGCAATA
AATCTGTTCCTGGTGGCAACTGGAGGAGCAGATGCATGTTAGGAAATGGGCATTCACTGCTGGGATACGGCAGGAGCTGG
TGTTATCATTAATGAAGCTGGTGGAGTGTTTTTGGATATAACAGGGGGACCTTTTGACTTGATGTCATGAAGAATAATTG
CTGCAAGCATCAGAGTCTTAGCAGAAAGAATTGCCAAAGAAATTCAGCTAATACCTCTTCAGCGAGATGATGAAGAG
ORF - retro_mdom_1310 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.93 % |
| Parental protein coverage: | 77.26 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SHSFIGEESVAAGEHSVLTDNPTWIIDPIDGTTNFVHRFPFVAISIGFVVGKKMEFGVVYSCIEDKMYTG |
| SHSFIGEESVAAG.HSVLTDNPTWIIDPIDGT.NFVHRFPFVAISIGF.VGKKMEFGVVYSCIEDKMYTG | |
| Retrocopy | SHSFIGEESVAAGDHSVLTDNPTWIIDPIDGTINFVHRFPFVAISIGFDVGKKMEFGVVYSCIEDKMYTG |
| Parental | R-KGKGAFCNDQKLHVSGQEDITKSLLVTELGSNRQPEVVKTILSNMERLLCIPIHGIRAAGTAAINMCL |
| R.K..G.F...............K..LVTEL..NRQPEVVKT.LSNME.L..IPIHGIR.AGTAAIN..L | |
| Retrocopy | R>KENGLFAMIKNFMCQDKKILLK--LVTELVVNRQPEVVKTFLSNMEILFYIPIHGIRGAGTAAINLFL |
| Parental | VATGGADAYYEMGIHCWDMAGAGVIVTEAGGVLLDITGGPFDLMSQRIIAASSRVLAERIAKEIQLIPLQ |
| VATGGADA..EMGIHCWD.AGAGVI..EAGGV.LDITGGPFDLMS.RIIAAS.RVLAERIAKEIQLIPLQ | |
| Retrocopy | VATGGADAC*EMGIHCWDTAGAGVIINEAGGVFLDITGGPFDLMS*RIIAASIRVLAERIAKEIQLIPLQ |
| Parental | RDDEE |
| RDDEE | |
| Retrocopy | RDDEE |
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_1310 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1310 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000023030 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000002628 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000006271 | 1 retrocopy |
retro_mdom_1310 ,
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