Sequence
atgc intronic sequence ATGC exonic sequencegtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttttcatgaaatgtccctgcccttattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
Basic information
species | Glycine max |
transcript | GLYMA05G26240.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os08g10600.3 (Oryza sativa), 3'ss of exon 14
gtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttt-tcatgaaatgtccctgccctta-ttcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
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-------------------------------------------------------------------------------------gtaacgttttgtatgtatatctagaaacttttgaagaccgtcactagctgaaatttttttagatggaaatttgtgaattgattatcgcataactttacttgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCATATGCCGTGGACGGACATTCCATGCACCGAGTGAGATTTCATTTTAGGA
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 14
lower sequence: AT2G35020.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttttcatgaaatgtccctgcccttattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
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----------------------------------------------------------------------------------------------------------------------gtaaagagccccatccaactcttcttttcagttgattcttttactt--cactaacactcatagc--ttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G31070.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttttcatgaaatgtccctgcccttattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
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----------------------------------------------------------------------------------------gtaactctcaaaacaaatcttctcattactgtgtttttatttattttacttttctgtccaacgaatttatttttcttatatgcaaaatc--gaataaattttagGTGTAGAGGTTTCACCTTTGTGCTCATACGCCGGAGAAAATCTTGAAGCTATTTGTCGAGGAAGAACGTTTCATGCACCTTGTGAAATTTCCCTCTAATG
upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 14
gtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttttc---atgaaatgtccctgcccttatt--------cagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
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-----------------------------------------------------------------------------------------------------ataaatc-atacataat-tcttctcattttcaatggtagtggcactaacagactcatattctatttgatatgtggtgtggcggtgtttgatgtggaggccagGTGTGGAGATATCACCACTCTGCTCCTATTCTGGGGAAAACCTAGAAGCCATCTGCCGTGGAAGAACATTTCACGCTCCTTGTGAAATCTCATTCTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatggtcttatctaactctttttcttttcatgaaatgtccctgcccttattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
atctaac putative branch site (score: 2)
tccctgcccttattc putative PPT
tttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttttcatgaaatgtccctgcccttattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC