RetrogeneDB ID: | retro_mdom_962 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:38795912..38796592(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ENDOU | ||
| Ensembl ID: | ENSMODG00000009733 | ||
| Aliases: | None | ||
| Description: | endonuclease, polyU-specific [Source:HGNC Symbol;Acc:14369] |
Retrocopy-Parental alignment summary:
>retro_mdom_962
CTCTACAGCTGCGTAAATGGAGAACTCTTCTCCAAACTAGCGTATGCTGCATTCATCAGTCTACTCAATAACTACCACCG
GCTAACAGGCCAGGGGGGACACTTCCATTCTCAGCACCTTGAGGAACAGGACACTTTTCTTCCAGAGATAATGAAGTCAA
TAGTCATGAAGGAACTCAATGGTTTCCTCCATCAAAAAAACACATACAGCTCCGAGCAAGAATTTGTCAGTGACAGGAAG
AAGATGTGGATGGGGTTGTATTCCCGGGGCCAGGATGAGGGTGACTCCAGTGGCTTTGAACACGTTTTCTCTGGTGAAGT
GAAAAAGGGAAAAGTGTCAGATTCCATGGCTGGATCCACTTCTACCTGCAGGAGGAGGGTCTGGTCGACTATTACAGCCA
CAACTATGACGGGCCGTGGGACTCGTATCCTGATGTGCTAGGAATGCAATTCAACTGGGATGGCAACTTCAAAGAAGTGG
GATCGACGTTCATGGGCAGTCCGGAGTGTGAATTTGCCCTCTCTTCCTTGTGCTTCATCAGCAGACCTGGCGGTGTGTGT
CATTTGAGCCCCGGGGTGGGGGGGCACCCCCTGGCTATCCAAATCTAGACCTGGGCCACAGTGACCTATGGAAATGGCAA
GAAGTACTTTGCCAAAGCCTATATAGTATCTTCTACGGAT
ORF - retro_mdom_962 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.04 % |
| Parental protein coverage: | 55.5 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LYSYVNEELFSKPTYAAFISLLNNYHRVTGQGEHFSSQQLEEQDTFLREIMKTAVMKELYGFLHQKNRYS |
| LYS.VN.ELFSK..YAAFISLLNNYHR.TGQG.HF.SQ.LEEQDTFL.EIMK..VMKEL.GFLHQKN.YS | |
| Retrocopy | LYSCVNGELFSKLAYAAFISLLNNYHRLTGQGGHFHSQHLEEQDTFLPEIMKSIVMKELNGFLHQKNTYS |
| Parental | SEQEFVSDLKKMWFGLYSRGHDEGDSSGFEHVFSGEVKKGKVSG-FHNWIRFYLQEKEGLVDYYSHNYDG |
| SEQEFVSD.KKMW.GLYSRG.DEGDSSGFEHVFSGEVKKGKVS..FH.WI.FYLQE.EGLVDYYSHNYDG | |
| Retrocopy | SEQEFVSDRKKMWMGLYSRGQDEGDSSGFEHVFSGEVKKGKVSD<FHGWIHFYLQE-EGLVDYYSHNYDG |
| Parental | PWDSYPDVLGMQFNWDGYFKEVGSAFIGSSPEFEFALYSLCFISRPGGVCHLS--LGGYPLAIKTYTWDK |
| PWDSYPDVLGMQFNWDG.FKEVGS.F.G.SPE.EFAL.SLCFISRPGGVCHLS...GG.PLAI...TW.. | |
| Retrocopy | PWDSYPDVLGMQFNWDGNFKEVGSTFMG-SPECEFALSSLCFISRPGGVCHLSPGVGGHPLAIQI*TWAT |
| Parental | VTYGNGKKYIATAYIVSSTN |
| VTYGNGKKY.A.AYIVSST. | |
| Retrocopy | VTYGNGKKYFAKAYIVSSTD |
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_962 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_962 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 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000009733 | 2 retrocopies |
retro_mdom_1285, retro_mdom_962 ,
|