RetrogeneDB ID: | retro_mmus_2504 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:115303399..115303678(-) | ||
| Located in intron of: | ENSMUSG00000066071 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mcts1 | ||
| Ensembl ID: | ENSMUSG00000000355 | ||
| Aliases: | Mcts1, 1500019M23Rik, MCT-1 | ||
| Description: | malignant T cell amplified sequence 1 [Source:MGI Symbol;Acc:MGI:1916245] |
Retrocopy-Parental alignment summary:
>retro_mmus_2504
TATTCTTTTATCTTATCACAACAGTGGATTAATAAAAGAGTCATTAAACTTGTACTTAGTGGATCAAATATCATGTTTCC
AGGGTTAACATCTGGGTCTAAGCTTTACCCTGCTGCAGAAGATACTATTTTTGCAAACGTGTCAGAAGGAAAGAAACATG
CTGTATGTATTGGAGTCCTGAAAATATATGCAGAACATTTTGAGAAAGTCAACAAAGGAATTAGCATTGAAAATATCCAT
TATTTAAATGATATGCTATGACATAGGGAGATATATAAA
ORF - retro_mmus_2504 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.96 % |
| Parental protein coverage: | 51.93 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | YPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQHALCVGVMKMSAEDIEK |
| Y.FIL..Q...K..IK.VLSG.NIM.PGLTS.G.KLYPAA.DTI.A...EGK.HA.C.GV.K..AE..EK | |
| Retrocopy | YSFILSQQWINKRVIKLVLSGSNIMFPGLTS-GSKLYPAAEDTIFANVSEGKKHAVCIGVLKIYAEHFEK |
| Parental | VNKGIGIENIHYLNDGLWHMKTYK |
| VNKGI.IENIHYLND.L.H...YK | |
| Retrocopy | VNKGISIENIHYLNDML*HREIYK |
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 | 27 .01 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 14 .46 RPM |
| SRP007412_heart | 0 .00 RPM | 8 .44 RPM |
| SRP007412_kidney | 0 .00 RPM | 14 .51 RPM |
| SRP007412_liver | 0 .00 RPM | 14 .53 RPM |
| SRP007412_testis | 0 .00 RPM | 1 .69 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2504 was not detected
No EST(s) were mapped for retro_mmus_2504 retrocopy.
No TSS is located nearby retro_mmus_2504 retrocopy 5' end.
retro_mmus_2504 was not experimentally validated.