RetrogeneDB ID: | retro_mdom_1389 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:258461991..258462378(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000011375 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1389
AGACAAAGGAAGCAGCATGAAGAAATGAAATTGGTCCTCACAATGGCCTATCCAATCACCAAAATACAAATAGAATTCAA
AAACCAGAGCAGGAAAAAAAAATCTCTAGTAGCTCATTTTCTGCCACATATGCCTCATGTAAGTGAACGCCTGATGAAAA
GAAGTTTAAAGTCTGATGACCTGAGATATTTGACATCTGGGTAGCTACAAGTGCTAGTCAATGACCCCCCACTCCTGGGT
AGAGAGCATGAATGAAGAGACAGTTCAGCTGTTTCTCATTTGAGATGGATTGAATGCAGAACAAGATAATGTCGTTTAAC
ACAGAAGATTTTAACTGGCCTTGCTATAAGTTAGCAGAAATTCATGGCTAAGAAAATGCATATGAAA
ORF - retro_mdom_1389 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.2 % |
| Parental protein coverage: | 51.82 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RQRKLQAEAKMALAMAKPMAKMQVEVEKQNRKK-SPVADLLPHMPHISECLMKRSLKPTDLRDMTIGQLQ |
| RQRK...E.K..L.MA.P..K.Q.E...Q.R...S.VA..LPHMPH.SE.LMKRSLK..DLR..T.G.LQ | |
| Retrocopy | RQRKQHEEMKLVLTMAYPITKIQIEFKNQSRXXXSLVAHFLPHMPHVSERLMKRSLKSDDLRYLTSG*LQ |
| Parental | VIVND-LHSQIESLNEELVQLLLIRDELHTEQDAML-VDIEDLTRHAESQQKHLAEKMPAK |
| V.VND..HS..ES.NEE.VQL.LI.D.L..EQD.........LT..A.S.QK..A.KM..K | |
| Retrocopy | VLVND>PHSWVESMNEETVQLFLI*DGLNAEQDNVV<LTQKILTGLAIS*QKFMAKKMHMK |
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_1389 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1389 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 | ENSMODG00000011375 | 1 retrocopy |
retro_mdom_1389 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000014607 | 1 retrocopy |