Sequence
atgc intronic sequence ATGC exonic sequencegtaatctatttttaataatacttctgtttaaatgcgtcaacaaattatgagcatcttacattttccgaattcacatatgccattgctaatgtgtccaacttggttgaatttgcattctaatcaaaattctgttatattcattaattacagGATTGTCTAAGCTAACTTCTGATTCCAGATCAGCAATCCGTAAAAGCTCCTTGGAAGTGCTCTTTAATATTTTGAAGGATCATGGCCATATTTTTTCACG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38200.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G00230.1 (Glycine max), 3'ss of exon 10
gtaatctatttttaataatacttctgtttaaatgcgtcaacaaattatgagcatcttacattttccgaattcac-atatgccattgctaatgtgtccaacttggttgaatttgcattctaatcaaaattctgttatattcattaattacagGATTGTCTAAGCTAACTTCTGATTCCAGATCAGCAATCCGTAAAAGCTCCTTGGAAGTGCTCTTTAATATTTTGAAGGATCATGGCCATATTTTTTCACG
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-----------------------------------------------tgatttaaccacattttgtgcagcagtgagataacataaattccataact--cttgtctgttctttctgctttaagttaatatttttatatt--ttcattgcagGGTTATCAAAACTAACTTCTGATCCAAGATCAGCTATCAGAAAGAGTTCTTTGGAGATGCTTTTTAACATTTTGAAGGATCATGGTCATCTATTCTCCCA
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G48200.1 (Glycine max), 3'ss of exon 9
gtaatctatttttaataatacttctgtttaaatgcgtcaacaaattatgag-catcttacattttccgaattcacat-atgccattgcta-atgtgtccaacttggttgaatttgcattctaa-tcaaaattctgttatattcattaattacagGATTGTCTAAGCTAACTTCTGATTCCAGATCAGCAATCCGTAAAAGCTCCTTGGAAGTGCTCTTTAATATTTTGAAGGATCATGGCCATATTTTTTCACG
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-----------------------------------------------tgagataacataaactccataaggatatttcaggccatttttccataactcttgcctgttc---tttatactttaagttaatatttttatattttcattga----agGGTTATCAAAACTAACTTCTGACCCAAGATCAGCTATCAGAAAGAGTTCTTTGGAGGTGCTTTTTAACATTTTGAAGGATCATGGTCATCTATTCTCCCA
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0038g04090.t01 (Vitis vinifera), 3'ss of exon 9
gtaatctatttttaataatacttctgtttaaatgcgtcaacaaattatgagcatcttacattttccgaattcacatatgccattgctaatgtgt--ccaacttggttgaatttgcattctaatcaaaattctgttatattcat-taattacagGATTGTCTAAGCTAACTTCTGATTCCAGATCAGCAATCCGTAAAAGCTCCTTGGAAGTGCTCTTTAATATTTTGAAGGATCATGGCCATATTTTTTCACG
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-----------------------------------------------------tttaattttgttattaagcacctttgatgttgcaaatttattacaaagattttgtcttttccgttctcaagtaatatatattttgcaaatgttgtttcagGATTGTCAAAGCTAACATCTGATCCCAGATCAGCTATCAGAAAAAGTTCTTTGGAAGTGCTTTTTAACATCCTAAAGGATCATGGTCATCTTTTTTCACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacttggttgaatttgcattctaatcaaaattctgttatattcattaattacagGATTGTCTAAGCTAACTTCTGATTCCAGATCAGCAATCCGTAAAAGCTCCTTGGAAGTGCTCTTTAATATTTTGAAGGATCATGGCCATATTTTTTCACG
attctaatcaaaattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctatttttaataatacttctgtttaaatgcgtcaacaaattatgagcatcttacattttccgaattcacatatgccattgctaatgtgtccaacttggttgaatttgcattctaatcaaaattctgttatattcattaattacagGATTGTCTAAGCTAACTTCTGATTCCAGATCAGCAATCCGTAAAAGCTCCTTGGAAGTGCTCTTTAATATTTTGAAGGATCATGGCCATATTTTTTCACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG