RetrogeneDB ID: | retro_mdom_1346 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:94232605..94233350(-) | ||
| Located in intron of: | ENSMODG00000018493 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000018480 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1346
GTAAACAACAGAAATAGAAAAAAGAAATCACAATTGACAGCTTCTATCCAGGCAATGAAGAAAGAGCAAATGAAACAGAG
AAGGATCAAGGAACACCAAGCAAAAACAAAGAAACTCCAGTGATTGGACACAGGCTTTGGAAGAACTCAAAATACAATTC
AAAAAATAATTAGAGGCTGAAGAGAACTGGGAAAAGAACTTAAAAAGCAAAATAAGTCATCTGGAAACAGAAAATAGTGT
CTTGAAAGACAAAATTAATCAGCTTGAAAATGAGGCAAAGGAGATGAAAGATGTCCTCCAAAGAAAATCGGACTAGAAGG
AGAAGGATGACCAAAGAGCCAGGGATGAAATTCAGTCTTTAAAAACTAGAATACAACAACTAGAAGAAAACGACTTCACA
AGGAAGCAGGAAACTATAAAACAAATTCAAAGAATGAAAAAATTGAGGAAAATATGAAACATCTCATCCATAAAACAGAA
GATTTAGAAAAACCAAGAAAACTCCCCCGACATTCTGGAGCAAGAGAGAAAAGGGGAGATTGAAAGAATCCACAGATCAC
CTCCTGTACTTAATCCCCAACTGACAACACCCAGGAATGTTATTGCCAAATTCAAGAACTACCAGACCAAGGAAAAAATA
TTACAAGCTGCTAAGAAGTCATTCAGATACCATGGAACTATAGTTAGGATAACACAGGATCTGGCTGCATCTACACTGAA
GGACCAAATGGCATGGAATGATATT
ORF - retro_mdom_1346 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.51 % |
| Parental protein coverage: | 75.38 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LNPKDKKGTNTLSRAQKNLLEQSKRKQR-GRTQQRKKSEIPGNWIQALEELKMQSKTQLREAEDNWEKNL |
| .N....K....L..A..........KQR.G......K......W.QALEELK.Q.K..L.EAE.NWEKNL | |
| Retrocopy | VNNRNRKKKSQLT-ASIQAMKKEQMKQR>GSRNTKQKQRNSSDWTQALEELKIQFKK*L-EAEENWEKNL |
| Parental | KTKISHLETENSVLKAKINQLENEAKEMKDEAKQMKDEVKKMKDDLQRKSDQKENMKHLIHKTEDLENRS |
| K.KISHLETENSVLK.KINQLENEAKEMKD......D...K.KDD.QR..D.....K..I...E...... | |
| Retrocopy | KSKISHLETENSVLKDKINQLENEAKEMKDVLQRKSD*--KEKDD-QRARDEIQSLKTRIQQLEENDFTR |
| Parental | RRDNLRIIGLPEDHDKRKSLDIILQEIIK--ENCPKILEQEGKVETDRIHRSPPVLNPQLTTPRNVIAKF |
| .......I.......K......I.Q.I.K..EN.P.ILEQE.K.E..RIHRSPPVLNPQLTTPRNVIAKF | |
| Retrocopy | KQETIKQIQRMKKLRKI*NISSIKQKI*KNQENSPDILEQERKGEIERIHRSPPVLNPQLTTPRNVIAKF |
| Parental | KDYQ----ILQAAKKKSLRYQGTTVRITQDLAASTLKKRKAWNTI |
| K.YQ....ILQAA.KKS.RY.GT.VRITQDLAASTLK...AWN.I | |
| Retrocopy | KNYQTKEKILQAA-KKSFRYHGTIVRITQDLAASTLKDQMAWNDI |
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_1346 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1346 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000018480 | 3 retrocopies |
retro_mdom_1071, retro_mdom_1072, retro_mdom_1346 ,
|