RetrogeneDB ID: | retro_mmus_3278 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:56437613..56438282(+) | ||
| Located in intron of: | ENSMUSG00000032329 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ube2s | ||
| Ensembl ID: | ENSMUSG00000060860 | ||
| Aliases: | Ube2s, 0910001J09Rik, 6720465F12Rik, AA409170, E2-EPF | ||
| Description: | ubiquitin-conjugating enzyme E2S [Source:MGI Symbol;Acc:MGI:1925141] |
Retrocopy-Parental alignment summary:
>retro_mmus_3278
ATGAACTCCAATGTGGAGAATCTGCCGCCCCACATCATCCGCCTAGTGTACAAGGAGGTGACAACACTGACGGCAGACCC
ACCTGATGGCATTAAAGTCTTCCCCAATGAGGAGGATCTCACAGACCTGCAGGTTACCATCGAGGGCCCTGAAGGGACTC
CCTATGCTGGAGGTCTGTTCCGTATGAAGCTCCTACTGGGGAAGGACTTCCCTGCCTCCCCACCCAAGGGCTACTTCCTG
ACTAAAATCTTCCACCCAAATGTGGGCCCCAATGGCGAGATCTGTGTCAATGTGCTCAAGAGGGACTGGACGGCTGAATT
GAGCATACGACATGTGCTGCTGACCATCAAGTGCCTGCTGATCCACCCTAACCCAGAGTCTGCACTCAATGAGGAGGCAG
GCCGCCTGCTTTTGGAGAATTATGAAGAGTATGCTGCCCGGGCCCGTCTGCTCACAGAAATCCATGGGGGTGCATGCAGC
ACCAGCAGCGGGAGGGCTGAGGCTACCCAAGACCTGGCCAGTGGGGCTTCAGCCTCCTCTGCTGACCCTATGATCCCAGG
GGTCCTAGGGGGAGCTGAGGGTCCCATGGCCAAGAAACATGCAGGTGAGCGAGATAAGAAGCTGGCAGCCAAGAAAAAGT
TGGACAAGAAGCGAGCACTGAGGCGACTG
ORF - retro_mmus_3278 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.55 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF |
| MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF | |
| Retrocopy | MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF |
| Parental | PASPPKGYFLTKIFHPNVGPNGEICVNVLKRDWTAELGIRHVLLTIKCLLIHPNPESALNEEAGRLLLEN |
| PASPPKGYFLTKIFHPNVGPNGEICVNVLKRDWTAEL.IRHVLLTIKCLLIHPNPESALNEEAGRLLLEN | |
| Retrocopy | PASPPKGYFLTKIFHPNVGPNGEICVNVLKRDWTAELSIRHVLLTIKCLLIHPNPESALNEEAGRLLLEN |
| Parental | YEEYAARARLLTEIHGGACSTSSGRAEATQDLASGASASSADPMIPGVLGGAEGPMAKKHAGERDKKLAA |
| YEEYAARARLLTEIHGGACSTSSGRAEATQDLASGASASSADPMIPGVLGGAEGPMAKKHAGERDKKLAA | |
| Retrocopy | YEEYAARARLLTEIHGGACSTSSGRAEATQDLASGASASSADPMIPGVLGGAEGPMAKKHAGERDKKLAA |
| Parental | KKKLDKKRALRRL |
| KKKLDKKRALRRL | |
| Retrocopy | KKKLDKKRALRRL |
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 .12 RPM | 7 .45 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 5 .47 RPM |
| SRP007412_heart | 0 .28 RPM | 8 .81 RPM |
| SRP007412_kidney | 0 .06 RPM | 7 .49 RPM |
| SRP007412_liver | 0 .03 RPM | 4 .29 RPM |
| SRP007412_testis | 0 .87 RPM | 62 .53 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3278 was not detected
No EST(s) were mapped for retro_mmus_3278 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_151375 | 131 libraries | 250 libraries | 109 libraries | 121 libraries | 461 libraries |
| TSS #2 | TSS_151376 | 224 libraries | 413 libraries | 403 libraries | 30 libraries | 2 libraries |
The graphical summary, for retro_mmus_3278 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_3278 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3278 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000874 | 3 retrocopies | |
| Homo sapiens | ENSG00000108106 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000020390 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000060860 | 2 retrocopies |
retro_mmus_1675, retro_mmus_3278 ,
|
| Pan troglodytes | ENSPTRG00000011507 | 2 retrocopies | |
| Rattus norvegicus | ENSRNOG00000016930 | 2 retrocopies |