RetrogeneDB ID: | retro_mdom_607 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:506745949..506746364(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SFT2D2 | ||
| Ensembl ID: | ENSMODG00000002896 | ||
| Aliases: | None | ||
| Description: | SFT2 domain containing 2 [Source:HGNC Symbol;Acc:25140] |
Retrocopy-Parental alignment summary:
>retro_mdom_607
TTGACTAAAGTAACTAAAACAGCATAATTAAGTTAGGGCACAAGAATAAGAGACTTTGCTGCTTATTTTACTTTAGGGAT
TCTTTTCTTGTCCCTGGTACTTTTCTGCTACAGATGCCTTGGAAAGGCTTTATCTTTTTTTGCAGTATTTTATGCCTTGG
GGAACACTGCATCACCTGAGAGTATTCTTTCTTATGGGACCAATGAAGCAGCTGAAATGTATGTTTAAGTCTACTTGACA
GATATGCACCAATGTGATGCTGTTGCATCTTGTATTCACCCTATGTTATGCCTTCTGGTGGCACAACAAAGAACTTGTTC
TCATTTTCTGCATTTCAGGGTCTTTGGCCTTGAAGTGGTACATATAGCCTTTCTTTTATATCACTTGGAAGGGATGCTGT
GAAAAGAAATGTTTT
ORF - retro_mdom_607 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.23 % |
| Parental protein coverage: | 84.05 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LAEVIETPSLSWGTRIKGFAACFAIGIIFSLM-GTFFLWVPKKGLVLF-AAFYTL-GNIASLGSTIFLMG |
| L..V..T..LS.GTRI..FAA.F..GI.F....GTF.L..P.KG...F.A.FY.L.G....L....FLMG | |
| Retrocopy | LTKVTKTA*LS*GTRIRDFAAYFTLGILFLSL<GTFLLQMPWKGFIFF>AVFYAL>GTLHHL-RVFFLMG |
| Parental | PVKQLKRMFETTRLIATIVMLLCLILTLCSAFWWHNKGLALIFCILQSLALTWY--SISYIPFARDAVKK |
| P.KQLK.MF..T..I.T.VMLL.L..TLC.AFWWHNK.L.LIFCI..SLAL.WY.....YI.......KK | |
| Retrocopy | PMKQLKCMFKST*QICTNVMLLHLVFTLCYAFWWHNKELVLIFCISGSLALKWYI*PFFYITWKGCCEKK |
| Parental | CF |
| CF | |
| Retrocopy | CF |
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_607 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_607 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 8 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000010720 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000016838 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000002896 | 1 retrocopy |
retro_mdom_607 ,
|
| Mustela putorius furo | ENSMPUG00000000531 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000014912 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000003038 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000018938 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000022560 | 1 retrocopy |