Sequence
atgc intronic sequence ATGC exonic sequencegtcctatcaatttcttctttcttttctctgttttgatcggcaaattttggttatttgttttgtttttaaacggattgggtttaatctcagtttcttcttcttggtttgggttgtggtttatgatcagATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGGAAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G02830.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G38650.1 (Glycine max), 3'ss of exon 1
gtcctatcaatttcttctttcttttctctgttttgatcggcaaattttggttatttgttttgtttttaaacggattgggtttaatctcagtttcttcttcttggtttgggttgtggtttatgatcagATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGGAAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAAC
| | | | | ||| ||| | | | | || ||| | || | | | | ||| || | || ||| |||| ||||||||||||||||||| || ||||| ||| ||||||||||||| | || |||| ||||| | |||||||| || |||||||| || ||||| || ||
------------------gtttgtagtacactgagataaataaagtgagaaatagaagtctaaattaaaatga--tgtctctttttgagagatggacttgttcatatga--tgttgttt-----cagATGCAATGTGGCAAATTAACTTGAGGTCAAGTGAAACAATGGAATCAGGACCTTATCCTGAGCATCCAGGAGAACCAGATTGTTCATACTACATTAGGAC
upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 1
gtcctatcaatttcttctttcttttctctgttttgatcggcaaattttggttatttgttttgtttttaaacggattgggtttaatctcagtttcttcttcttggtttgggttgtggtttatgatcagATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGGAAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAAC----------------------------------------------------------
| || | || ||| |||| ||||||||||||||||||| || ||||| ||| ||||||||||||| | || |||| ||||| | |||||||| || |||||||| || ||||| || ||
--------------------------------------------------------------------------------------------------tgttcatatga--tgttgttt-----cagatgcaatgtggcaaattaacttgaggtcaagtgaaacaatggaatcaggaccttatcctgagcatccaggagaaccagATTGTTCATACTACATTAGGACTGGCCTTTGTAGATTTGGAGCAACATGTCGATTTAATCATCCTCCTAACAGGAAGCTG
upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 1
gtcctatcaatttcttctttcttttctctgttttgatcggcaaattttggttatttgttttgtttttaaacggattgggtttaatctcagtttcttcttcttggtttgggttgtggtttatgatcagATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGGAAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAAC-
| | | | | ||| ||| | | | | || ||| | || | | | | ||| || | || ||| |||| ||||||||||||||||||| || ||||| ||| ||||||||||||| | | |||| ||||| | |||||||| || |||||||| || ||||| || ||
-------------------tttgtattacactgagataaataaagtgagaaatagaagtctaaattaaaatga--tgtctctttttgagagattgacttgttcatatga--tgttgttt-----cagaTGCAATGTGGCAAATTAACTTGAGGTCAAGTGAAACAATGGAATCAGAACCTTATCCTGAGCATCCAGGAGAACCAGATTGTTCATACTACATTAGGACT
upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 1
gtcctatcaatttcttctttcttttctctgtt-ttgatcggcaaattttggttatttgttttgtttttaaacggattgggtttaatctcagtttcttcttcttggtttgggttgtggtttatgatcagATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGGAAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAAC
|||| || || ||| | || | | | ||| |||||| | | | | | ||||| | | ||| | || | | ||| |||||||||||||||||||||| ||||| || |||||||||||| |||| |||| || || || || ||||| || || |||||||| ||||| || ||
--------------------ctttgaaagattatttatctgaaattacttcctctttagtttgttat-acgggaagtatttttaaaagatgatctgacttact--ttcctatcattgttc-----cagATGCAATGTGGCAAATGAACTTGAGATCGAGTGAAACAATGGAGTCTGGACCTTATCCCGAGCGTCCGGGAGAACCAGACTGTTCTTACTACATCAGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgggtttaatctcagtttcttcttcttggtttgggttgtggtttatgatcagATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGGAAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAAC
gtttaat putative branch site (score: 4)
tttaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcctatcaatttcttctttcttttctctgttttgatcggcaaattttggttatttgttttgtttttaaacggattgggtttaatctcagtttcttcttcttggtttgggttgtggtttatgatcagATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGGAAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC