RetrogeneDB ID: | retro_mdom_1644 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 6:36158599..36159289(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TXNDC15 | ||
| Ensembl ID: | ENSMODG00000014348 | ||
| Aliases: | None | ||
| Description: | thioredoxin domain containing 15 [Source:HGNC Symbol;Acc:20652] |
Retrocopy-Parental alignment summary:
>retro_mdom_1644
TATTCTCTAACTACATCTGGAACAAATATTCCTGATAAGGGAGAAGAATGTAATTTGGTTCTTGAAGCTGTGCCCACAAG
CCCATCATCTAAAGAAGACTATAATAGTACAGACAATGTAAAGACTCCAAAGGTGAATTGTGAGGAGAGAAATGTTACTG
GCTTAGAAAGTTTCACTTTACAAATTCTAAATGTTTCACAGGACCTGATGGAATTTTGAAACCCAAACAGTAGTGATTAT
ACATTAGTCTTATTTTATACTCCTTGGTGTCGCTTTTCTGCCAGTCTGGCCCCACATTTTAATTCTTTACCATGTGCATT
TCCATCTCTTCATTTTTTGGCATTGGATGCTTCTCAGCACAGCAGTCTGTCTACCCGGTTTGGTACTGTGGCTGTTCCCA
ACATCTTGCTATTTCAAGGAGCTAACCCAATGGCGAGATTTAATCATCCAGATTGGACTCTGGAAACTCTAAAAGCCTTC
ATTTTTAATCAGACAGGGATAGAAGCCAGAAATGATGTGGTGGTGACTGAAGATGACCAAATAAGCCCTCTTCCCAGCAC
CTTGGTGAAAAGTGTGGATTGGTTGCTTGTATTTTCTTTATTCTTTTTAATTAGTTTTATTATGTATGCTACTGTTCAGA
CTGAAAGTATTTGATGGCTCATTCCAGGACAAGAACATGAACATCCTGAG
ORF - retro_mdom_1644 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.78 % |
| Parental protein coverage: | 67.85 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FSLTTSGTNIPDKGEEYNLVLEAVPTSPSSKEDSNSTDNVKTPKVNCEERNVTGLESFTLQILNVSQDLM |
| .SLTTSGTNIPDKGEE.NLVLEAVPTSPSSKED.NSTDNVKTPKVNCEERNVTGLESFTLQILNVSQDLM | |
| Retrocopy | YSLTTSGTNIPDKGEECNLVLEAVPTSPSSKEDYNSTDNVKTPKVNCEERNVTGLESFTLQILNVSQDLM |
| Parental | EFLNPNSSDCTLVLFYTPWCRFSASLAPHFNSLPRAFPSLHFLALDASQHSSLSTRFGTVAVPNILLFQG |
| EF.NPNSSD.TLVLFYTPWCRFSASLAPHFNSLP.AFPSLHFLALDASQHSSLSTRFGTVAVPNILLFQG | |
| Retrocopy | EF*NPNSSDYTLVLFYTPWCRFSASLAPHFNSLPCAFPSLHFLALDASQHSSLSTRFGTVAVPNILLFQG |
| Parental | AKPMARFNHTDRTLETLKAFIFNQTGIEARNDVVVTEDDQIGPLPSTLVKSVDWLLVFSLFFLISFIMYA |
| A.PMARFNH.D.TLETLKAFIFNQTGIEARNDVVVTEDDQI.PLPSTLVKSVDWLLVFSLFFLISFIMYA | |
| Retrocopy | ANPMARFNHPDWTLETLKAFIFNQTGIEARNDVVVTEDDQISPLPSTLVKSVDWLLVFSLFFLISFIMYA |
| Parental | TVRTESIRWLIPGQEHEHPE |
| TV.TESI.WLIPGQEHEHPE | |
| Retrocopy | TVQTESI*WLIPGQEHEHPE |
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 | 193 .46 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 119 .16 RPM |
| SRP007412_heart | 0 .00 RPM | 153 .70 RPM |
| SRP007412_kidney | 0 .00 RPM | 161 .97 RPM |
| SRP007412_liver | 0 .00 RPM | 194 .85 RPM |
| SRP007412_testis | 0 .00 RPM | 83 .29 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1644 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1644 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000014348 | 3 retrocopies |
retro_mdom_1644 , retro_mdom_646, retro_mdom_759,
|
| Tupaia belangeri | ENSTBEG00000015609 | 1 retrocopy |