RetrogeneDB ID: | retro_mdom_1511 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:75726292..75726847(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C6orf136 | ||
| Ensembl ID: | ENSMODG00000015898 | ||
| Aliases: | None | ||
| Description: | chromosome 6 open reading frame 136 [Source:HGNC Symbol;Acc:21301] |
Retrocopy-Parental alignment summary:
>retro_mdom_1511
GTGTCTCTTCCTTCTGGGAAGGGGGAGGATGGACCAGGGCTAGGATTGCACAGAGGCAGCCTGGAGGAGCTTAGAAGCCT
CTCTGAAGAATTGCCTTGCCCCTATCCTGGGACTCTGATGTCATTCCAGGTCCCTAAAAGTCCTCACCCTGCTCCTGCCA
CTCCCTCAGAGACCCACAGCATGGAGGAAAATCTAGCCATCATGAATGAGAAACTGAGGCAGGAGCTCCCTAGCCTGTCT
CTTCCCTCCCACAATTACAACCTCTACTCATCTGATGTGGAATTCATCAGAGAGATTCTGCACATTTGAAGCAAAGGCCA
CACATGATATATTCTATCATTGACCCTCTGCCAATTCTTGGCCAGGGATTATTCTGCTCAGGTGCAGCTGGAAGTCCTTA
GGGTAAGCCAACATCCTGAAGACTGCATACTGCAGGCACACTGGTGGCTTGAGGGTTTGCCTACCCATCTCCTCTTCCTG
CACTTCCACCACCAGGACAAGGATGAACTTTACCAGACATAGGATGCATATTCTATTTTCTACCTAAACTCCAAA
ORF - retro_mdom_1511 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.27 % |
| Parental protein coverage: | 58.18 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VGLPSEKGEDGQGPGLHGGCLDGLRSLFEELPCPHPGAVIPFRAPGSPHPSPATPSGNPNMEEHLAVMHE |
| V.LPS.KGEDG.G.GLH.G.L..LRSL.EELPCP.PG....F..P.SPHP.PATPS....MEE.LA.M.E | |
| Retrocopy | VSLPSGKGEDGPGLGLHRGSLEELRSLSEELPCPYPGTLMSFQVPKSPHPAPATPSETHSMEENLAIMNE |
| Parental | KLRQELPNLFLRSHDYNLYSSDVEFINEILNIRTKGRTWYILSLTLCRFLAWNYFAQLQLEVLRLSQHPE |
| KLRQELP.L.L.SH.YNLYSSDVEFI.EIL.I..KG.T.YILSLTLC.FLA..Y.AQ.QLEVLR.SQHPE | |
| Retrocopy | KLRQELPSLSLPSHNYNLYSSDVEFIREILHI*SKGHT*YILSLTLCQFLARDYSAQVQLEVLRVSQHPE |
| Parental | DWTLQARWRLVGLPTHLLFLRFYRRDKDDLYRTYDAYSTFYLNSE |
| D..LQA.W.L.GLPTHLLFL.F...DKD.LY.T.DAYS.FYLNS. | |
| Retrocopy | DCILQAHWWLEGLPTHLLFLHFHHQDKDELYQT*DAYSIFYLNSK |
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_1511 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1511 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 | |
|---|---|---|---|
| Felis catus | ENSFCAG00000007692 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000015898 | 1 retrocopy |
retro_mdom_1511 ,
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