RetrogeneDB ID: | retro_mmus_3656 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:87519323..87519770(-) | ||
| Located in intron of: | ENSMUSG00000052372 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dppa4 | ||
| Ensembl ID: | ENSMUSG00000058550 | ||
| Aliases: | Dppa4, 2410091M23Rik, C76608, ECAT15-1 | ||
| Description: | developmental pluripotency associated 4 [Source:MGI Symbol;Acc:MGI:2157525] |
Retrocopy-Parental alignment summary:
>retro_mmus_3656
GGGTGGAAGTCTTAGGTGACAGTTCCTCTTGAAATGGTCCCCATACCAGAGGAGCTGTACTTGTCCTGACTGAACCTCCT
GTGTTTTATGAGGAAGTCAGGACCACTGTTGTGACTACAACTGCCTCCAATGCAGTGTTGATGTCTTGGGCCAGAATTGC
AGCCAACACTAAAAGTATCAAGGCAATGTATTCCAATGCAACACCTGCACCTGAGACCTATGAGGGAAATGTGTGTGGTT
CATGGGAAAAGCCTTCCTGTAACCTCAAGTGGTTGGGTTCAGCTGCAGTTCCATTGCAGACAAGCCTGGGTACCTGAGAA
GAAAGGGAAAGTAATTGCCCTCTTCATGCTTCCAGCTTACACATTTCAACCCTCACACATAGATGACAAAATGTTGTGCC
CCTTGTATGGTCAGAGAAACAAGGTCTTAACTAAGAGTCTTGAAGGA
ORF - retro_mmus_3656 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.53 % |
| Parental protein coverage: | 61.48 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GEESEVTVPLEMVPVPEE-QIPALIDPPMLYEEVSTTVVTTPATEAVLASWARIASNAKKYEAVPADASS |
| G..S.VTVPLEMVP.PEE.....L..PP..YEEV.TTVVTT.A..AVL.SWARIA.N.K...A....A.. | |
| Retrocopy | GWKS*VTVPLEMVPIPEE<AVLVLTEPPVFYEEVRTTVVTTTASNAVLMSWARIAANTKSIKAMYSNATP |
| Parental | SSEV-KGEMWCVVHGTSLPGNSRGWVRLQFHAGQAWVPDKKGKAIALFLLPACTFPPPHLEDNMLCPKCV |
| ..E....EM..V.HG.SLP..S.GWV.LQFH..QAWVP.KKGK.IALF.LPA.TF.P.H..D.MLCP... | |
| Retrocopy | APET>MREMCVV-HGKSLPVTSSGWVQLQFHCRQAWVPEKKGKVIALFMLPAYTFQPSHIDDKMLCPLYG |
| Parental | HKNKILTKSLEG |
| ..NK.LTKSLEG | |
| Retrocopy | QRNKVLTKSLEG |
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 .07 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 .04 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 1 .28 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3656 was not detected
No EST(s) were mapped for retro_mmus_3656 retrocopy.
No TSS is located nearby retro_mmus_3656 retrocopy 5' end.
retro_mmus_3656 was not experimentally validated.