Sequence
atgc intronic sequence ATGC exonic sequence...atgactattggtttctaattgatttaagtatatcatttattctggtatctgctaagatatttcatggcaaccttttcatttattctgtctaattttacagAATGAATATTCAGAACAATGGGCTATGGCATGTGGTGAAATTTTGCGTATTTTAACTCATTACAATCGCCCCATATACAAAATGGAAAGGCAATATTGTG
Basic information
species | Glycine max |
transcript | GLYMA09G07240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 4
atgactattggtttctaattgat-ttaagtatatcatttatt---ctggtatctgctaagatatttcatggcaaccttttcatttattctgtctaattttacagAATGAATATTCAGAACAATGGGCTATGGCATGTGGTGAAATTTTGCGTATTTTAACTCATTACAATCGCCCCATATACAAAATGGAAAGGCAATATTGTG
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----------gtatataatagctgtctagtatcatgcttactgatttggtgtaacctataccattttgtgctaacatgttca----------ctatcctaacagAATGACTATTCGGAGCAATGGGCTTTGGCATGTGGAGAAATCCTTCGCATTTTGACTCATTACAACCGTCCCATTTATAAAACTGAGCAGCAAAATGGAG
upper sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------atgactattggtttctaattga--------tttaagtat--atcatttattctggtatctgctaagatatttcat--ggcaaccttttcatttattctgtctaattttacagAATGAATATTCAGAACAATGGGCTATGGCATGTGGTGAAATTTTGCGTATTTTAACTCATTACAATCGCCCCATATACAAAATGGAAAGGCAATATTGTG
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gtatgtcgtgctggcatgactgaacaaatttgagttgctctgctttcaaatatcttgctcatgctattttttctttcttgttaaactgtagttttgggttttagaaacttattcccaattcttatgtgattgatgagtggacaagagatcgtgatacatttttctaaattgcagAATGAGTATTCTGAACAATGGGCTCTGGCATGTGGGGAGATTTTGCGAATTTTAACTCATTACAATCGCCCAATTTACAAGGTGGAACATCAGAGCAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctgctaagatatttcatggcaaccttttcatttattctgtctaattttacagAATGAATATTCAGAACAATGGGCTATGGCATGTGGTGAAATTTTGCGTATTTTAACTCATTACAATCGCCCCATATACAAAATGGAAAGGCAATATTGTG
gtctaat putative branch site (score: 3)
ttttcatttattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgactattggtttctaattgatttaagtatatcatttattctggtatctgctaagatatttcatggcaaccttttcatttattctgtctaattttacagAATGAATATTCAGAACAATGGGCTATGGCATGTGGTGAAATTTTGCGTATTTTAACTCATTACAATCGCCCCATATACAAAATGGAAAGGCAATATTGTG
- - ctattgg
- - - - - - - - - - - - - - - - - - - attctgg
- - - - - - - - - - - - - - - - - - - - - - - -tctgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggca