Sequence
atgc intronic sequence ATGC exonic sequencegtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaagcttctttactttgaaatgtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
gtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaa-gcttctttactttgaaatgtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
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-----cttttgatgctata-taaacaattttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 8
gtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaagcttctttactttgaaatgtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
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---aaaaatatatagttgagaattttgcatctttatatgggatgttcttatattcttcctagcaactagtggccttgtttttactgtct--ttgttgttaaatagGTACAAGACCCAGACTTGACTGGTGTTAGTCATTTGCTGGTGGATGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 6
gtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaagcttct--ttactttgaaat-gtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
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---aaaaatatatagttgagaattttg-tatccgt-atatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaa---tagGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 6
gtaagatacaactattctactactcaactactcatcacatgtagttgaagtatg-atattttaagcttctttactttgaaatgtcgaatcaatt-gttg--aaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
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---------tgtcatttgaaggattagttgttgtataagcatactgggatggcacacacattctgatgttttcttttccattctcttatgattttgatgttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATTCATGAAAGAGGCATGAATGAGGACTTCCTTTTAATAATTTTGCATGACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgatattttaagcttctttactttgaaatgtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
tattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaagcttctttactttgaaatgtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA