Sequence
atgc intronic sequence ATGC exonic sequencegtaacaacttgtatattcttaatttcttctcttccattacttcaaacgaaaaaaacatgggagagagcttcttaactcattccatggtgaatttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
Basic information
species | Glycine max |
transcript | GLYMA17G09310.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G09310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g36460.1 (Oryza sativa), 3'ss of exon 1
--gtaacaacttgtatattcttaat-ttcttctcttccattacttcaaacgaaaaaaacatgggagagagcttcttaactcattccatggtga-atttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
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tgtttatatcgta-atttagttgctatacctctctctttgtatctcactctctgacagtgtgtga-ataatataatgtgtgttgctgagttgctgtgtacagGATTGGAGAGGTGTGGCAAGAGTTGCAGGCTGAGATGGATCAACTACCTGAGGCCTGATCTCAAGAGAGGCAGCTTCTCCCAGCAGGAGGAGGAGCTCAT
upper sequence: GLYMA17G09310.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g09080.t01 (Vitis vinifera), 3'ss of exon 1
gtaacaacttgtatattcttaatttcttctcttccattacttcaaacgaaaaaaacatgggagagagcttcttaactcattccatggtgaa-tttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
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--------------gtaattaatttctcttcttc----accttccacattttcatctttcttggtagttggtaaattgttttgatggtgatctttgtagGTTTGCAGAGGTGCGGAAAGAGTTGCAGATTGAGATGGATTAACTATTTGAGACCCGACCTTAAGAGAGGAATGTTCTCTCAGCAAGAGGAGGATATCAT
upper sequence: GLYMA17G09310.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
-----gtaacaacttgtatattcttaatttcttctcttccattacttcaaacgaaaaaaacatgggagagagcttcttaactcattccatggtgaatttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
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tttcctctttgctctaaaaaaagaaaagttcagataccccgttgacaccaatttagaata---agagttgtgtcgctgacgctggtgtgccctggaacaacagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGAT
upper sequence: GLYMA17G09310.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
gtaacaacttgtatattcttaatttcttctcttccattacttcaaacgaaaaaaacatgggagagagcttcttaactcattccatggtgaatttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
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------------------gtgagtatttgtacctca--atttcaagtt-------ctcgtgag-----ctcacaattc--ttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacgaaaaaaacatgggagagagcttcttaactcattccatggtgaatttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
tcttaac putative branch site (score: 2)
aaaaaaacat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaacttgtatattcttaatttcttctcttccattacttcaaacgaaaaaaacatgggagagagcttcttaactcattccatggtgaatttgcagGACTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGAAAGAGGAGGATCTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT