Sequence
atgc intronic sequence ATGC exonic sequencegtagttagattctaaaatccacctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatactttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatctttttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G14100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
gtagttagattctaaaatccacctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatactttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatct--ttttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
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-------------------------------------------------------------gtatatttttttgcttagttatctctttgtc--taatttcttaatttaaat--tttaaaga-----------------ctagctgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 3
gtagttagattctaaaatccacctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatactttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatct--ttttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
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-------------------------------------------------------------gta--tatctttttttagctaagt-tatgtct----ttgtctaattt-gttaatttaa-------attttaaaaactagtta---aaagtggagctttatatttgacatttggtgtctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 3
gtagttagattctaaaatccac-ctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatact--ttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatctttttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
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----------------gtatattcttctttatgctatcttgttaa-------tttttggattgtacctgttaagctgaagatctgtatggaaaagttattagacttctcacatgttagtttagcattctatcccttactttgctggtttatcatcatat--tgacatctccattgattctcctcggtgcagTCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCT
upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S84_50V6.1 (Physcomitrella patens), 3'ss of exon 4
gtagttagattctaaaatccacctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatactttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatctt-tttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
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------------------------------------------------------------------------------------tttaactgaatgtttcttgacatt--atactttaaggaagtt--ttcaatt-ctttcgagtcgcattggggtttgatagttcatttcgtgttttttttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATMapped 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|124832370|gb|EH916809.1|EH916809EST: TAAACTCATCAGAAAGGATAAG TCATCATATGGATTTGTTCAC-ACTTTGATCGAAGATCCGCTGCTCTGGCT
genomic: TAAACTCATCAGAAAGGATAAGgtagttagat ... ttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctgcttactaaaaatggactcataaagcatgcatctttttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
tactaaa putative branch site (score: 1)
tctttttatttattt putative PPT
atctttttatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttagattctaaaatccacctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatactttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatctttttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
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