Sequence
atgc intronic sequence ATGC exonic sequencegtatacattatttttcatcgcttgttgcttatgaatgatctgcattcacataagtttatatatgatttcttacaatttccattttgacttgtggtttgagtctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
Basic information
species | Glycine max |
transcript | GLYMA20G23660.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatacattatttttcatcgcttgttgcttatgaatgatctgcattcacataagtttatatatgatttcttacaatttccattttgacttgtggtttgagtctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
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-------------------------------------------------------------gtaactccct----cattaagtcaaaccttttctctttttctttctctgcaacttcg-agacatttatttcgaccttttacgttgccgtttcagGAAGCTTTAGATATTGTGCATGTTAGTAAAGAAGATCAAGAAAATGTATTTGCAATGCTTGCTGCAGTATTATGGCTAGGGAATGTTTCTTTTACCATTA
upper sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
gtatacattatttttcatcgcttgttgcttatgaatgatctgcattcacataagtttatatatgatttcttacaatttccattttgacttgtggtttgagtctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
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-------------------------------------------------gtaattctctctttcagttag-atactttcttcctcctcttctctactcatttcagacctttatttttctgtttattgatttaa--aagtttctgttg--ttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
upper sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
gtatacattatttttcatcgcttgttgcttatgaatgatctgcattcacataagtttatatatgatttcttacaatttccattttgacttgtggtttgagtctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
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----------------gtattttttcccttcttgatga-ctaaaccca-ata---ttaatcat--ttttgtacctattttcttct---ctatgatatggat---aaagggtggtgatgtgtgcatg---tacttgattttaatttt--ttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
ttttaat putative branch site (score: 3)
ctattttt CT-rich tract
ttttttcatgctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacattatttttcatcgcttgttgcttatgaatgatctgcattcacataagtttatatatgatttcttacaatttccattttgacttgtggtttgagtctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG