Sequence
atgc intronic sequence ATGC exonic sequencegttagtagttcctaaagaatgtctctgaagtgtgatctgacttttctttttttttggagcatattgtaccttttgatcataaaataatatctatttatctggcagAACAGGAAGGGCTTTCCTCTTTTAGTTAGTGGTGTTCCTCCTGACGCATTCAGTGAAACTGGTCAGCTTTGGGGCAG
Basic information
species | Glycine max |
transcript | GLYMA04G39730.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39730.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g43390.1 (Oryza sativa), 3'ss of exon 7
gttagtagttcctaaagaatgtctctgaagtgtgatctgacttttctttttttttggagcatattgtaccttttgatcataaaataatatctatttatctggcagAACAGGAAGGGCTTTCCTCTTTTAGTTAGTGGTGTTCCTCCTGACGCATTCAGTGAAACTGGTCAGCTTTGGGGCAG
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----gtacacctcaataattttccctcata-gtcatgtgtcatcggattctt-----aaaatgctatacattctgtttcttgattgtttttt-ctggtgtaa-agGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG
upper sequence: GLYMA04G39730.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G64860.1 (Arabidopsis thaliana), 3'ss of exon 7
gttagtagttcctaaagaatgtctctgaagtgtgatctgacttttctttttttttggagcatattgtaccttttgatcataaaataatatctatttatctg---gcagAACAGGAAGGGCTTTCCTCTTTTAGTTAGTGGTGTTCCTCCTGACGCATTCAGTGAAACTGGTCAGCTTTGGGGCAG
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gcaagtaaattttaacatatggaggcaaa---cagttttatcatatgtaccaggaagaaaat-tagtctttcctgaaagtcgctctttttttgttttgctttacacagAACAAGAAAGGCTTTCCTCTTCTTGTTAGCGGTGTTCCTCCTGACTTGTTCAGTGAAACTGGTCAACTGTGGGGCAG
upper sequence: GLYMA04G39730.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01540.t01 (Vitis vinifera), 3'ss of exon 7
gttagtagttc-ctaaagaatgtctctgaagtgtgatctgacttttctttttttttggagcatattgtaccttttgatcataaaataatatctatttatctggcagAACAGGAAGGGCTTTCCTCTTTTAGTTAGTGGTGTTCCTCCTGACGCATTCAGTGAAACTGGTCAGCTTTGGGGCAG
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gttagtagttctcttcattaactttaagaaatcttaataatctagtcatgaccttc------cattctgagttctactgacaaatt---atccctttgt-tggcagAACAAGAGCGGTTTTCCTCTTCTAGTTAGTGGTGTTCCTCCCGATGCCTTTAGTGAAACTGGCCAGCTGTGGGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttggagcatattgtaccttttgatcataaaataatatctatttatctggcagAACAGGAAGGGCTTTCCTCTTTTAGTTAGTGGTGTTCCTCCTGACGCATTCAGTGAAACTGGTCAGCTTTGGGGCAG
ttttgat putative branch site (score: 4)
tctattt putative PPT
ttttgatcataaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtagttcctaaagaatgtctctgaagtgtgatctgacttttctttttttttggagcatattgtaccttttgatcataaaataatatctatttatctggcagAACAGGAAGGGCTTTCCTCTTTTAGTTAGTGGTGTTCCTCCTGACGCATTCAGTGAAACTGGTCAGCTTTGGGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT