RetrogeneDB ID: | retro_mdom_1695 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 6:255141389..255141762(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SPDYC | ||
| Ensembl ID: | ENSMODG00000010068 | ||
| Aliases: | None | ||
| Description: | speedy/RINGO cell cycle regulator family member C [Source:HGNC Symbol;Acc:32681] |
Retrocopy-Parental alignment summary:
>retro_mdom_1695
CTGCAGCTCAGTGTATACACCTACAGCAACCTCTTCTTAGCCCCGTATCTAGTGAATTACATAGAAGAAGACAGAGAAGA
CCCCAAGTATGAGATTTTTGTCCTGGGCCCTGGGCCAGGGCTGGTGGAAACTTGTGCCTAGCTTTTTGCACCAGGGGGAC
CAGTTGTGGGCATGTATGGGCTACAGGGCAGCTGTAAGGCAACACTGCTGTGAAGAGGTCATGGCAAAGGAACCGTCCCA
TTGGGCTTGGACAAGGGAGCGACCAGTCCACCATGGGGGTGCTCATCAAGGCTCCCCCCAGGAGCTCCAGAACTGCCCTT
CTGTCATGTCCCATGTCTCAAACCTCTCTCGACTGGGCTGCTTCCTTTGTGGC
ORF - retro_mdom_1695 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.8 % |
| Parental protein coverage: | 56.11 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LQLSEYTHSNLFLALYLANDMEEDREDPKYEI-LPWALGQGWRKLVPSFLRQRDQLWARMGYRAAVSRHC |
| LQLS.YT.SNLFLA.YL.N..EEDREDPKYEI.L.WALGQGW.KLVPSFL.Q.DQLWA.MGYRAAV..HC | |
| Retrocopy | LQLSVYTYSNLFLAPYLVNYIEEDREDPKYEI>LSWALGQGWWKLVPSFLHQGDQLWACMGYRAAVRQHC |
| Parental | CEEVMAKEPSHWAWTRERPIHHGGAQRSSLQGNQNCPSVMSHVSNLSPLGCSVCG |
| CEEVMAKEPSHWAWTRERP.HHGGA...S.Q..QNCPSVMSHVSNLS.LGC..CG | |
| Retrocopy | CEEVMAKEPSHWAWTRERPVHHGGAHQGSPQELQNCPSVMSHVSNLSRLGCFLCG |
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_1695 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1695 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 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002403 | 2 retrocopies | |
| Monodelphis domestica | ENSMODG00000010068 | 3 retrocopies |
retro_mdom_1043, retro_mdom_1348, retro_mdom_1695 ,
|
| Otolemur garnettii | ENSOGAG00000015020 | 1 retrocopy |