>retro_mmus_713
ATGAAATCCGAAGCCAAGGATGGAGAGGAGGAAAGTCTGCAAACTGCCTTCAAGAAATTAAGAGTGGACGCATCAGGGTC
CATCATATCTCTGTCTGTTGGAGAAGGCCCAAGTGTCAGAGCATCAGCCAGAACAGCAGCCGATGATACCAAACCGAAAA
CCATGTGTGCATCTAAAGACAGTTGGCATGGGTCTACAAGGAAGTCTTCACAAGGAGCAGTGAGAACCCAGCGTCGTAGA
CGGTCTAAGTCTCCTGTTCTTCATCCTCCCAAATTCATAAATTGCAGTACAACAGCACCTCCTTCCAGCAGCCAGCTTAA
GCACAGAAGCCAGACTGAGCCACCCGATGGCATCAGTGGACGGGGAATTTCAACACCCAAAGAGTTCAACGCAGGAGAAA
ACTCTACTTCTCTTGATGTTAATCACACAGGAGCAGCCATCGAGCCTCTGAGAAGCTCGGTTCTGAGGCTCCCATCAGAG
AGTAAAACAGAAGAGCTCTCTGATGCTACCCAAGTCTCCCAAGAAAGTCTTACGGCTAACGATCTCTCTGACTTTCAATC
TGTTTCCAAGCTAAGTCAGGGCAAGCCATGTGTGTGTGTAGGCAAGGAGTGCCAGTGTAAGAGGTGGCATGACATGGAAG
TGTATTCCTTTTCAGGTCTGCAGAATGTCCCTCCTCTGGCCCCAGAACGAAGATCACTTGAGGACTACTCTCAGTCACTG
CACACCAGAACTCTGTCTGGCTCGCCTCGATCCTGTTCCGAGCAAGCTCGTGTCTATGTGGATGATGTGACCATTGAGGA
CCTAGCAGGCTACATGGAGTATTACTTGTATATCCCTAAGAAAATGTCCCACATGGCAGAGATGATGTACACC
ORF - retro_mmus_713 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
99.31 % |
Parental protein coverage: |
100. % |
Number of stop codons detected: |
0 |
Number of frameshifts detected |
0 |
Retrocopy - Parental Gene Alignment:
Parental | MKSEAKDGEEESLQTAFKKLRVDASGSIISLSVGEGPSVRASARTAADDTKPKTMCASKDSWHGSTRKSS |
| MKSEAKDGEEESLQTAFKKLRVDASGSIISLSVGEGPSVRASARTAADDTKPKTMCASKDSWHGSTRKSS |
Retrocopy | MKSEAKDGEEESLQTAFKKLRVDASGSIISLSVGEGPSVRASARTAADDTKPKTMCASKDSWHGSTRKSS |
|
Parental | RGAVRTQRRRRSKSPVLHPPKFIHCSTTAPPSSSQLKHRSQTEPPDGISGRGISTPKEFNAGENSTSLDV |
| .GAVRTQRRRRSKSPVLHPPKFI.CSTTAPPSSSQLKHRSQTEPPDGISGRGISTPKEFNAGENSTSLDV |
Retrocopy | QGAVRTQRRRRSKSPVLHPPKFINCSTTAPPSSSQLKHRSQTEPPDGISGRGISTPKEFNAGENSTSLDV |
|
Parental | NHTGAAIEPLRSSVLRLPSESKTEELSDATQVSQESLTANDLSDFQSVSKLSQGKPCVCVGKECQCKRWH |
| NHTGAAIEPLRSSVLRLPSESKTEELSDATQVSQESLTANDLSDFQSVSKLSQGKPCVCVGKECQCKRWH |
Retrocopy | NHTGAAIEPLRSSVLRLPSESKTEELSDATQVSQESLTANDLSDFQSVSKLSQGKPCVCVGKECQCKRWH |
|
Parental | DMEVYSFSGLQNVPPLAPERRSLEDYSQSLHTRTLSGSPRSCSEQARVYVDDVTIEDLAGYMEYYLYIPK |
| DMEVYSFSGLQNVPPLAPERRSLEDYSQSLHTRTLSGSPRSCSEQARVYVDDVTIEDLAGYMEYYLYIPK |
Retrocopy | DMEVYSFSGLQNVPPLAPERRSLEDYSQSLHTRTLSGSPRSCSEQARVYVDDVTIEDLAGYMEYYLYIPK |
|
Parental | KMSHMAEMMYT |
| KMSHMAEMMYT |
Retrocopy | KMSHMAEMMYT |
|
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 |
2 .92 RPM |
SRP007412_cerebellum |
0 .00 RPM |
4 .30 RPM |
SRP007412_heart |
0 .03 RPM |
2 .65 RPM |
SRP007412_kidney |
0 .00 RPM |
3 .97 RPM |
SRP007412_liver |
0 .00 RPM |
4 .12 RPM |
SRP007412_testis |
0 .23 RPM |
41 .03 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_713 was not detected
3 EST(s) were mapped to retro_mmus_713 retrocopy
EST ID |
Start |
End |
Identity |
Match |
Mis-match |
Score |
BE627692 |
54401093 |
54401231 |
97.9 |
135 |
3 |
132 |
BQ632986 |
54401450 |
54401685 |
99.2 |
232 |
2 |
230 |
CF104782 |
54401079 |
54401262 |
100 |
183 |
0 |
183 |
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_13720 | 463 libraries | 106 libraries | 447 libraries | 48 libraries | 8 libraries |
TSS #2 |
TSS_13721 | 225 libraries | 555 libraries | 282 libraries | 9 libraries | 1 library |
The graphical summary, for retro_mmus_713
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_713 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_713 has 0 orthologous retrocopies within eutheria group .
Parental genes homology:
Parental genes homology involve
3 parental genes, and
3 retrocopies.