Sequence
atgc intronic sequence ATGC exonic sequence...aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
Basic information
species | Glycine max |
transcript | GLYMA16G17590.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggag-caaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
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-gtatttgaactactcaaaacaatc----tctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
upper sequence: GLYMA16G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
--aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
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gtattttaactactcaaaacaatctctatatcttcatgacattcaaagctggaacat------gagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
upper sequence: GLYMA16G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattat-cctgtaggagcaaagactga--caatacttagcattt-gaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
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---tttcatag-aaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|298184450|gb|HO029663.1|HO029663EST: TTTGTGTCTCTTCCTAACGGAGGAAATGATCTTAAGAGAATTCGCTTCAG CCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGGATTA
genomic: TTTGTGTCTCTTCCTAACGGAGGAAATGATCTTAAGAGAATTCGCTTCAGgtataatagt ... gaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTA
EST:
gi|298165508|gb|HO011557.1|HO011557EST: TTTGTGTCTCTTCCTAACGGAGGAAATGATCTTAAGAGAATTCGCTTCAG CCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTA
genomic: TTTGTGTCTCTTCCTAACGGAGGAAATGATCTTAAGAGAATTCGCTTCAGgtataatagt ... gaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
gactgac putative branch site (score: 2)
atttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - aaacaaa
- - - - - - - - - -gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgaca