RetrogeneDB ID: | retro_mdom_1836 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 8:42851346..42852372(+) | ||
| 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: | ENSMODG00000022818 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1836
AGGCTTAGGAACATGGAGCCCAAAGGTTTAATCGAGAACTTCAAAGGTGATCTCACTTGCTCCATCTGTCTGGGCTACTT
CAGCAAACCAGGGACTGTCAAATATGGGTACAGTTTTGCAGAAAGTGTCTCCTCCAGTGCAGTGAGGAATCTGATGGTAC
ATTAATCTATCCAGAGTGCAGAGGAATCATTAGATACAGTTATATCATGCCCAACAAGAACCTGCAGAATCTATCCATCA
CTGGCAAAACTCTCTGACCAAATTTACTGCTGAGCACAGTACTTCTGACTATCTGTGATCAAAATGGGGAAAAGAGAAGC
TATTTTGTGAGGAAGAGGAAAAACTAATTTGAGGTTCCTACTTAGTAACCCAAGAGCACAAGGATCACCAAGTCCTTTCC
TTGCAAATGGCTGACAAGTGAAAGGAGAAACTCAGGAGACATTGAATTTCTTACAAGAAAAAGTGGAGAAATTTAAAATT
GCATTGAACAATGTGAGAATGAAAGAGGCACAACATAAGGAGAAATTTTGTGTTCTTAAACAATCAATTATGTGTGAATA
TGGTAAAATGCACCAGTTCATATGGGATGAAGAATATCAATACCTGAACAGCCTGGAGCAAGATTCAGAAGACAACCTGG
CAAATTTCAACAAAAATGAGGCTAAATTGACCCAACAAATCCAACATCTGCAACAAATGATATTATAAATAGAGGATAAT
TTGGAGAAGGCACCCTTGGAAATGCTCCAGGTTATGAAAGCCACCTTGAAAAAGGATGAGAAACTGCTAGTTCAAGAACC
AGAGGTTGTTTCCATTGAGTGGACCAGCACTTCATCACTGGTTTAAGAGAAAAGCTCTTGACCTTTTACGGGGATATTTC
TCTAAAACATGAAACATCCTATCTTTCTCTCATTCTGCCTGAAATTTTAAAAAATGCCAAGAATGGACATGCCCCCAGAA
GACCAGGCTGACCAGGAAGAAAGACTTGATTATGTTATTAATGTATTGGGAACTCAGATAGTCACT
ORF - retro_mdom_1836 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.71 % |
| Parental protein coverage: | 74.51 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | RLRNMEAKELIESLKAELTCSICLGYFTDPVTALKCGHTF-CKDCLLQCDEQADATLTCPECRAVIRYSD |
| RLRNME.K.LIE..K..LTCSICLGYF..P.T..K.G..F.C..CLLQC.E..D.TL..PECR..IRYS. | |
| Retrocopy | RLRNMEPKGLIENFKGDLTCSICLGYFSKPGT-VKYGYSF<CRKCLLQCSEESDGTLIYPECRGIIRYSY |
| Parental | IVPNENLQNLSITGKTLRQHLLLSPALLTTCDQHGKK-EKLFCEQDQKPICDSCLLTQEHKDHQDLPLQM |
| I.PN.NLQNLSITGKTL...LLLS..LLT.CDQ.G.K.EKLFCE...K.I..S.L.TQEHKDHQ.L.LQM | |
| Retrocopy | IMPNKNLQNLSITGKTL*PNLLLSTVLLTICDQNGEK<EKLFCEEEEKLI*GSYLVTQEHKDHQVLSLQM |
| Parental | AADKCKKNL-QETLNVLQQKEEELKAEINNILKEEKYFKKDSDFYKELIRCEYRKMHEILYNEENRHLQK |
| A.DK.K..L.QETLN.LQ.K.E..K...NN....E...K......K..I.CEY.KMH.....EE...L.. | |
| Retrocopy | A-DK*KEKL<QETLNFLQEKVEKFKIALNNVRMKEAQHKEKFCVLKQSIMCEYGKMHQFIWDEEYQYLNS |
| Parental | LDQEIEDKLAKVEANKAKLSQQIQHVQQKILEIEESLDEAPLEMLQDMKGILERNEELQLQDTETVKLTY |
| L.Q..ED.LA....N.AKL.QQIQH.QQ.IL.IE..L..APLEMLQ.MK..L...E.L..Q..E.V.... | |
| Retrocopy | LEQDSEDNLANFNKNEAKLTQQIQHLQQMIL*IEDNLEKAPLEMLQVMKATLKKDEKLLVQEPEVVSIEW |
| Parental | TT-YQVTGLIEILRSYQTGITVDPETDRLHLIVPEHFKSLK-YRLDPRNQPENEERLDYFVIMLGTETFT |
| T.....TGL.E.L......I....ET..L.LI.PE..K..K.....P..Q...EERLDY....LGT...T | |
| Retrocopy | TS<HFITGLREKLLTFYGDISLKHETSYLSLILPEILKNAK>MDMPPEDQADQEERLDYVINVLGTQIVT |
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_1836 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1836 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 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000001670 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000022818 | 2 retrocopies |
retro_mdom_129, retro_mdom_1836 ,
|
| Tursiops truncatus | ENSTTRG00000012631 | 1 retrocopy |