Sequence
atgc intronic sequence ATGC exonic sequencegtaattgtttacaataaatcacacttcaagacattatgagttaacaataatgttcttatatcttcttggattgcagAGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
------------gtaattgttt--acaataaatcacacttcaagacattatg-------agttaacaataa--tgttcttatatcttcttggat-tgcagAGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGG
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tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
upper sequence: AT5G40540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0066g00370.t01 (Vitis vinifera), 3'ss of exon 3
-----------------gtaattgtttacaataaatcacacttcaagacattatgagttaacaataat-------gttcttatatcttcttggattgcagAGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGG
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gaattatgttttagatgcaaaatatcattgatgaagtgattcccaaaagaggcagatatgataataagcttgacaattttttttccttcccttttcccagAAAACTTGATCCTGACTGCAGATCACAAAACTGTCAAACTTGCGGATTTTGGCTTAGCCAGAGAAGAGTCATTAACAGAGATGATGACTGCCGAAACTGGMapped 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|116473897|gb|EG516489.1|EG516489EST: CGATCTCAAACCAG AGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTG
genomic: CGATCTCAAACCAGgtaattgttt ... tggattgcagAGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacttcaagacattatgagttaacaataatgttcttatatcttcttggattgcagAGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGG
agttaac putative branch site (score: 3)
ttcttatatcttctt putative PPT
ttaacaataatgttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgtttacaataaatcacacttcaagacattatgagttaacaataatgttcttatatcttcttggattgcagAGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG