RetrogeneDB ID: | retro_mmus_1765 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 18:33384397..33384955(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Osgep | ||
| Ensembl ID: | ENSMUSG00000006289 | ||
| Aliases: | None | ||
| Description: | O-sialoglycoprotein endopeptidase [Source:MGI Symbol;Acc:MGI:1913496] |
Retrocopy-Parental alignment summary:
>retro_mmus_1765
ATGCCCGCGGTACTGGGGTTCGAAGGCAGCGCCAACAAGATCGGCGTGGGCGTGGTCCGCGACGGCACGGTGCTGGCGAA
CCCGGGGCGCACTTATGTCACGGCCCCGGGCACGGGATTCTTTCCAGGTGACACGGCCAGGCACCATCGAGCTGTTATCC
TAGACCTACTGCAGGAGGCGCTAACAGAGACAGGATTAACCTCCAAGGACATTGATTGCATTGCTTTCACCAAAGGTCCT
GGCATGGGAGCCCCATTGGCTTCTGTAGCTGTTGTTGCCCGTACAGTGACCCAGTTGTGGAATAAGCCTTTGCTTGGCGT
GAACCACTGCATAGGCCACATTGAAATGGGCCGTCTCATCACTGGAGCCGTTAACCCAACTGTCCTGTATGTGAGCGGAG
GAAATACCCAGGTGATTTCCTACTCAGAACATCGTTATCGCATCTTTGGAGAAACTATTGATATCGCTGTGGGAAACTGC
CTGGATCGTTTTGCTCGGGTGCTGAAGATTTCCAATGACCCCAGTCCAGGCTACAACATTGACCAGATGGCAAAGCGG
ORF - retro_mmus_1765 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.77 % |
| Parental protein coverage: | 55.52 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPAVLGFEGSANKIGVGVVRDGTVLANPRRTYVTAPGTGFLPGDTARHHRAVILDLLQEALTEAGLTSKD |
| MPAVLGFEGSANKIGVGVVRDGTVLANP.RTYVTAPGTGF.PGDTARHHRAVILDLLQEALTE.GLTSKD | |
| Retrocopy | MPAVLGFEGSANKIGVGVVRDGTVLANPGRTYVTAPGTGFFPGDTARHHRAVILDLLQEALTETGLTSKD |
| Parental | IDCIAFTKGPGMGSPLASVAVVARTVAQLWNKPLLGVNHCIGHIEMGRLITGAVNPTVLYVSGGNTQVIS |
| IDCIAFTKGPGMG.PLASVAVVARTV.QLWNKPLLGVNHCIGHIEMGRLITGAVNPTVLYVSGGNTQVIS | |
| Retrocopy | IDCIAFTKGPGMGAPLASVAVVARTVTQLWNKPLLGVNHCIGHIEMGRLITGAVNPTVLYVSGGNTQVIS |
| Parental | YSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNIEQMAKR |
| YSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNI.QMAKR | |
| Retrocopy | YSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNIDQMAKR |
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 | 16 .00 RPM |
| SRP007412_cerebellum | 0 .48 RPM | 13 .68 RPM |
| SRP007412_heart | 0 .06 RPM | 25 .09 RPM |
| SRP007412_kidney | 0 .48 RPM | 18 .60 RPM |
| SRP007412_liver | 0 .19 RPM | 14 .15 RPM |
| SRP007412_testis | 0 .41 RPM | 12 .58 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1765 was not detected
No EST(s) were mapped for retro_mmus_1765 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_58523 | 558 libraries | 181 libraries | 317 libraries | 14 libraries | 2 libraries |
The graphical summary, for retro_mmus_1765 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_1765 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1765 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000014460 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000006289 | 1 retrocopy |
retro_mmus_1765 ,
|
| Oryctolagus cuniculus | ENSOCUG00000005020 | 1 retrocopy |