RetrogeneDB ID: | retro_mmus_790 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:52116491..52116743(-) | ||
| Located in intron of: | ENSMUSG00000097219 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lyrm2 | ||
| Ensembl ID: | ENSMUSG00000045854 | ||
| Aliases: | None | ||
| Description: | LYR motif containing 2 [Source:MGI Symbol;Acc:MGI:1917573] |
Retrocopy-Parental alignment summary:
>retro_mmus_790
GCGGCTTCCCGCTTGCCTCCTGCGGCCCTGACGCTGAAGCAGTTCATGAGAAGGCAGCAAGTTCTCCTCCTCTACAGAAA
GATTTTGCGAGCGATTAGGCAAGTTCCAAGTGATTCTGACTAAAAATACCTTTAGGACTGGGCCAGGAAAGAATTTAAAA
GAAACAAAAGTGCCATAGAAGAGGATACAATGATGATTACCCAAGGCAATATGCAGCTAAAGGAACTAGAAAGGACGCTT
GCTTTAGCCAAC
ORF - retro_mmus_790 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.02 % |
| Parental protein coverage: | 97.73 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSDRKYLQDWAREEFKRNKSATEEDTIRMMITQ |
| AASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSD.KYL.DWAR.EFKRNKSA.EEDT..MMITQ | |
| Retrocopy | AASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSD*KYL*DWARKEFKRNKSAIEEDT--MMITQ |
| Parental | GNMQLKELERTLALAN |
| GNMQLKELERTLALAN | |
| Retrocopy | GNMQLKELERTLALAN |
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 .05 RPM | 8 .32 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 5 .78 RPM |
| SRP007412_heart | 0 .00 RPM | 15 .07 RPM |
| SRP007412_kidney | 0 .06 RPM | 18 .27 RPM |
| SRP007412_liver | 0 .08 RPM | 7 .13 RPM |
| SRP007412_testis | 0 .00 RPM | 11 .94 RPM |
RNA Polymerase II activity may be related with retro_mmus_790 in 1 libraries
| ENCODE library ID | Target | ChIP-Seq Peak coordinates |
|---|---|---|
| ENCFF001YKA | POLR2A | 11:52117260..52118181 |
No EST(s) were mapped for retro_mmus_790 retrocopy.
No TSS is located nearby retro_mmus_790 retrocopy 5' end.
| Experiment type: | PCR amplification |
|---|---|
| Forward primer: | GAAGTAGCCCTTCAGTACTTTG (22 nt long) |
| Reverse primer: | CTTCATTTACATTCTTGATTAGAGTG (26 nt long) |
| Annealing temperature: | 53 °C |
| (Expected) product size: | 417 |
| Electrophoresis gel image: |  |
| Additional comment: | Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR |
Retrocopy orthology:
Retrocopy retro_mmus_790 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 7 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000009916 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000012230 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000045854 | 2 retrocopies |
retro_mmus_474, retro_mmus_790 ,
|
| Otolemur garnettii | ENSOGAG00000034900 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000004324 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000016198 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000007420 | 1 retrocopy |