RetrogeneDB ID: | retro_mmus_1516 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:48749399..48750140(-) | ||
| Located in intron of: | ENSMUSG00000030775 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Twistnb | ||
| Ensembl ID: | ENSMUSG00000020561 | ||
| Aliases: | Twistnb, 2410173G11, 2810024J17Rik, D16Wsu83e | ||
| Description: | TWIST neighbor [Source:MGI Symbol;Acc:MGI:106292] |
Retrocopy-Parental alignment summary:
>retro_mmus_1516
AACCTTTTAGGTGTTCCTACTGCATATGATAACATCAGAGTTGTGGGTGAACTAGGAGATATTTATGATGATCAAGGACA
CATTCATCTTAACATTGAAGCAGATTTTGTTATTTTCTGCCCTGAGCCTGGGCAGACGTTAATGGGTACAGTTAATAAAG
TATCGTCTAGCCATATTGGCTGTCTAGTCCATGGATGTTTTAACGCCTCTATCCCTAAGCCTGAGCAGATGTCATATGAG
GAGTGGCAAACATTGGAGATACATGTAGGCGATGAACTGGAATTTGATGTATTTCGCTTAGATTCAGATTCTGCTGGAGT
ATTCAGCATTCGAGGAAAACTGAATACCACCAGTTTGCAACTTAAGCGCTCTGTAGTTTCTGAAGACGTAGCAGAAACTG
TCATTGAAGAGGTTGTTGAAAAAACTCCAAAGAAGAAAAAAAAGAAGAAGAAAGACAAAGATACAGACACATGTGGAACA
GTTGATAGTGCTACAGAGGTAGCAGATGTTACAGATGTCACGCCACAGGAAGAAACAGACATACCATGTAGTGATAATGT
GAATGACTTCTTTGAGGAAGAGCCAAAGAAGAAGAAAAAGAAGAAGAAAAGGCACCAGAAAGATCAGGACCCCATTTTCC
AAGCCAGTGACTCCAGTGGCTACCAGAGTGACCATAACAAGAAAAAAAAGAAAAGAAAGCACGGTGAAGAGGCTAACTTT
GAGTCACCTAAGAAGAGACAG
ORF - retro_mmus_1516 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.16 % |
| Parental protein coverage: | 74.55 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SLLGVPIAYDNIRVVGELGDIYDDQGHIHLNIEADFVIFCPEPGQTLMGTVNKVSSSHIGCLVHGCFNAS |
| .LLGVP.AYDNIRVVGELGDIYDDQGHIHLNIEADFVIFCPEPGQTLMGTVNKVSSSHIGCLVHGCFNAS | |
| Retrocopy | NLLGVPTAYDNIRVVGELGDIYDDQGHIHLNIEADFVIFCPEPGQTLMGTVNKVSSSHIGCLVHGCFNAS |
| Parental | IPKPEQMSYEEWQTLEIHVGDELEFDVFRLDSDSAGVFCIRGKLSTTSLQLKHSAVSEDVAET-VVEEVV |
| IPKPEQMSYEEWQTLEIHVGDELEFDVFRLDSDSAGVF.IRGKL.TTSLQLK.S.VSEDVAET...E.V. | |
| Retrocopy | IPKPEQMSYEEWQTLEIHVGDELEFDVFRLDSDSAGVFSIRGKLNTTSLQLKRSVVSEDVAETVIEEVVX |
| Parental | EKTPKKKKKKKDKDTDTCGTVDSVTEVADVTDVTPQEETDIPCSDNVNDFFEEEPKKKKKKKKRHQEDQD |
| ..............TDTCGTVDS.TEVADVTDVTPQEETDIPCSDNVNDFFE................QD | |
| Retrocopy | XXXXXXXXXXXXXXTDTCGTVDSATEVADVTDVTPQEETDIPCSDNVNDFFEXXXXXXXXXXXXXXXXQD |
| Parental | PIFQASDSSGYQSDHNKKKKKRKHSEEANFESPKKRQ |
| PIFQASDSSGYQSDHNK......H.EEANFESPKKRQ | |
| Retrocopy | PIFQASDSSGYQSDHNKXXXXXXHGEEANFESPKKRQ |
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 .02 RPM | 5 .86 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 5 .25 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .70 RPM |
| SRP007412_kidney | 0 .13 RPM | 5 .51 RPM |
| SRP007412_liver | 0 .03 RPM | 5 .52 RPM |
| SRP007412_testis | 0 .00 RPM | 3 .38 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1516 was not detected
No EST(s) were mapped for retro_mmus_1516 retrocopy.
No TSS is located nearby retro_mmus_1516 retrocopy 5' end.
retro_mmus_1516 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1516 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000019157 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000017730 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000020561 | 1 retrocopy |
retro_mmus_1516 ,
|