Sequence
atgc intronic sequence ATGC exonic sequence...ttttctttttcctctgctttatgtgtttgtggataaaacacacatttaagtttatgtatatggttatctaacatggtctgttgctcatgttgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTCTTTGCTCCATTTCTTGGAAACAAACTCTATGAATATATTGCCATTGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 1
ttttctttttcctctgctttatgtgtttgtggataaaacacacatttaagtttatgtatatggttatctaacatggtctgt-tgctcatg-ttgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTCTTTGCTCCATTTCTTGGAAACAAACTCTATGAATATATTGCCATTGGTG
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gctgcaaattgcctagtattattt--tagttttcatgttttagaattgaatatttgtgtattctcatatagttttttttccctgcttatgattcatgaacagGTCGTGGCTATAACAGTATTTTTCTTGCTATCTATAGCATATTATGCTTTCTTTGCTCCTTTTCTTGGAAAGGACATCTATGAATATTTGGCTATTGGTG
upper sequence: AT2G33640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G01810.1 (Glycine max), 3'ss of exon 1
ttttctttttcctctgctttatgtgtttgtggat--aaaacacacatttaagtttatgtatatggttatctaacatggtctgttgctcatgttgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTCTTTGCTCCATTTCTTGGAAACAAACTCTATGAATATATTGCCATTGGTG
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-caatgctgcaaattgccaagtattattttagtttcatgttttagaattggagatttgtgtattctcataaagctttttcccccctgcttatta-tgaacagGTCGTGGCTATAACTGTATTTTTCTTGCTATCTATAGCATATTATGCTTTCTTTGCTCCTTTTCTGGGAAAGGACATCTATGAATATGTGGCTATTGGTG
upper sequence: AT2G33640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 1
--ttttctttttcctctgctttatgtgtttgtggataaaacacacatttaagtttatgtatatggttatctaacatggtctgttgctcatgttgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTCTTTGCTCCATTTCTTGGAAACAAACTCTATGAATATATTGCCATTGGTG
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tgggagcatatgcgatcattctctttattcattgggataatatcc--tgccttttattagttttttgtgcttgtgtactcacccacttttttcaatgtgtagGTTGTGGCTATAACAGTCTTTTTCTTGCTATCTGTCGCATTTTATGCCTTTTTTGCTCCCTTCCTTGGGAAGGATATCTATGAATATGTGGCAATCAGTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116400824|gb|EG443416.1|EG443416EST: TTGTAATGGCGAGAAGACATGGATGGCAACTTCCAGCTCACACATTTCAA GTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCACTTACTATGCCTTC
genomic: TTGCAATGGCGAGAAGACATGGATGGCAACTTCCAGCTCACACATTTCAGgtttttttcc ... tgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTC
EST:
gi|116400803|gb|EG443395.1|EG443395EST: TTGCAATGGCGAGAAGACATGGATGGCAACTTCCAGCTCACACATTTCAG GTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTC
genomic: TTGCAATGGCGAGAAGACATGGATGGCAACTTCCAGCTCACACATTTCAGgtttttttcc ... tgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagtttatgtatatggttatctaacatggtctgttgctcatgttgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTCTTTGCTCCATTTCTTGGAAACAAACTCTATGAATATATTGCCATTGGTG
atctaac putative branch site (score: 2)
tttatgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttctttttcctctgctttatgtgtttgtggataaaacacacatttaagtttatgtatatggttatctaacatggtctgttgctcatgttgctgtgcagGTTGTTGCCATAACTGTATTTTTCTTGCTAACTGTCGCTTACTATGCCTTCTTTGCTCCATTTCTTGGAAACAAACTCTATGAATATATTGCCATTGGTG
- - - - - cctctgc
- - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - -aaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgc