Sequence
atgc intronic sequence ATGC exonic sequence...agtattaacatttataaactaactaagtcatcattttcttttaagttcctaattattgaagcactattgttattttaataatatttttactttattgtagGGTCACCGAATACCATGTGGATGGATTTCGATTTGATCTTGCAAGTGTCCTGTGTCGAGGAATTGATGGCTCCCCCCTCAATGCACCCCCACTTATTAGG
Basic information
species | Glycine max |
transcript | GLYMA06G10540.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g29404.3 (Oryza sativa), 3'ss of exon 1
agtattaacatttataaactaactaagtcatcattttcttt-taagttcctaattattgaagcactattgtta-ttttaataatatttttactttattgtagGGTCACCGAATACCATGTGGATGGATTTCGATTTGATCTTGCAAGTGTCCTGTGTCGAGGAATTGATGGCTCCCCCCTCAATGCACCCCCACTTATTAGG
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-taactgaattatagcatgcatttttattttctctttgacaatggttttgtcatatttcaaatgtcatttctaatctccatgcttgttttaatgcatca-agGGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 12
agtattaacatttataaactaactaagtcatcattttcttttaagttcctaattattgaagcactattgtt-attttaataatatttt----tactttattgtagGGTCACCGAATACCATGTGGATGGATTTCGATTTGATCTTGCAAGTGTCCTGTGTCGAGGAATTGATGGCTCCCCCCTCAATGCACCCCCACTTATTAGG
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----ttgttgatggtatctttatgatgaaactactttgatatatatttgta-ttattggatagccactcttcacactgttattcttttctactaaccaactgaagGGTCATTGAGTATCATGTGGATGGATTTCGATTTGATCTGGCTAGCGTTCTTTGTCGAGGAACAGATGGTTCTCCACTTAATGCTCCCCCAATTATTAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctaattattgaagcactattgttattttaataatatttttactttattgtagGGTCACCGAATACCATGTGGATGGATTTCGATTTGATCTTGCAAGTGTCCTGTGTCGAGGAATTGATGGCTCCCCCCTCAATGCACCCCCACTTATTAGG
tttttacttt CT-rich tract
aattattgaagcacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtattaacatttataaactaactaagtcatcattttcttttaagttcctaattattgaagcactattgttattttaataatatttttactttattgtagGGTCACCGAATACCATGTGGATGGATTTCGATTTGATCTTGCAAGTGTCCTGTGTCGAGGAATTGATGGCTCCCCCCTCAATGCACCCCCACTTATTAGG
- - - - - - - - - - - - - - - - - - - - - - gttccta