RetrogeneDB ID: | retro_mdom_1248 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:97696149..97696704(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KCTD13 | ||
| Ensembl ID: | ENSMODG00000015721 | ||
| Aliases: | None | ||
| Description: | potassium channel tetramerization domain containing 13 [Source:HGNC Symbol;Acc:22234] |
Retrocopy-Parental alignment summary:
>retro_mdom_1248
CCCCACTGCCTTATCCCTATGGTGACATCTCTAGGGAGGGACAGCAGCTTCTGGCTAGCACCACTAAGCCAATGGTGAAG
CTGCTGCACCATCAAAGTAACAACAAATACTCCTTATACCAGCATATCAGGCAACAACCTACTAAAGAAAATTGAGCTGT
CCAATATGCTGGCATTGTGCTTCCTCAGGTGGCTGCTCTTTCCCAAAGATGTACTGGGTGATAAAATCTGCTGCTGGTGG
TCTTTCTAAGGACAGAGTTAAAAGATTGCCAAAGTCTGCTGTACCTCCATTGTCTATACCACTTATAAGAAGCAAACCAA
GATGAAATTCCCAGAGGCAAGGATCTTTGAAGATACATCAAATATCCTGATCTGCAAGACAACCCAGGGGTCTGACCCTA
CTCTTCTAGAGTCCACTTGGGGTACTGCTGGAGGAGGTGGGTCTTAGCAAAGAGAAGATTAAGATGAATGGGAGCATCAA
GTATGAAGGATCCATGTCAGATGGCATATTATTCATGATGAATGACCCCACTGTCAGCAGGTTGTCATCAAGGAC
ORF - retro_mdom_1248 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.52 % |
| Parental protein coverage: | 61.54 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PLCLIPMVTS-PREEQQLLASTSKPVVKLLHNRSNNKYS-YTSTSDDNLLKNIELFDKLALRFHGRLLFL |
| P.CLIPMVTS..RE.QQLLAST.KP.VKLLH..SNNKYS.YTS.S..NLLK.IEL...LAL.F...LLF. | |
| Retrocopy | PHCLIPMVTS<SREGQQLLASTTKPMVKLLHHQSNNKYS>YTSISGNNLLKKIELSNMLALCFLRWLLFP |
| Parental | KDVLGDEICCW-SFYGQGRKIAEVCCTSIVYATEKKQTKVEFPEARIFEETLNILIYETPRGPDPALLEA |
| KDVLGD.ICCW.SF.GQ..KIA.VCCTSIVY.T.KKQTK..FPEARIFE.T.NILI..T..G.DP.LLE. | |
| Retrocopy | KDVLGDKICCWWSF*GQS*KIAKVCCTSIVYTTYKKQTKMKFPEARIFEDTSNILICKTTQGSDPTLLES |
| Parental | TGGAAGGGGAGRGEDEDGREHRVRRIHVRRHITHDERPHGQQAVFKD |
| T.G.AGGGG....ED.D..EH.V.RIHVR.HI.HDE.PH.QQ.V.KD | |
| Retrocopy | TWGTAGGGGS*QRED*DEWEHQV*RIHVRWHIIHDE*PHCQQVVIKD |
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_1248 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1248 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 | ENSMODG00000015721 | 1 retrocopy |
retro_mdom_1248 ,
|
| Monodelphis domestica | ENSMODG00000019235 | 1 retrocopy |