Sequence
atgc intronic sequence ATGC exonic sequence...tctatccaactattcatgagacgtataacccctgaatgttagatgagatctcagaatattatagaattctgtcatttatgtcttctctatcttaatgtagGTGCAAACTGATCTCCAGTATATTAAAGAAGATATAAATGCCGTTGAGAGACATAGAATAGATTTATACCGAGCTAGGGACAGATATTCTGTAAAGTTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 3
-------------tctatccaactattcatgagacgtata--acccctgaatgttagatgagatctcagaatattatagaattctgtcatttatgtcttctctatcttaatgtagGTGCAAACTGATCTCCAGTATATTAAAGAAGATATAAATGCCGTTGAGAGACATAGAATAGATTTATACCGAGCTAGGGACAGATATTCTGTAAAGTTGC
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gtttgtctatatgtatttttcagtatgcaggttttttttcttgctacctacaacaataaataatcttttactgatgtctattgttgttaatcatgttaacctcttttttacacagATTCAAACTGACCTACAGTACATCAAAGAAGATATAAGTGCTGTGGAGAGACATAGGTTAGAATTATATCGAACAAAAGAAAGGTACTCAATGAAGCTCC
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------------tctatccaactattcatgagacgta--taacccctgaatgttagatgagatctcagaatattatagaattctgtcatttatgtcttctctatcttaatgtagGTGCAAACTGATCTCCAGTATATTAAAGAAGATATAAATGCCGTTGAGAGACATAGAATAGATTTATACCGAGCTAGGGACAGATATTCTGTAAAGTTGC
|| | | | | | | | | || |||| | | | | |||| | | ||| | | | ||| ||| | | | ||||||| |||||||||||||||| ||| ||||| || || ||||| || |||| ||||||||| ||||| || || || ||||||| || |||||||| || |
gtgtgcttgctgcaatctctctccctctactctaaagtctaaactattgctaagtagctaatgtttcccattttttttctttcctgtgcttgcggtagttggtcattatttactactgatttccatgttacatct---atttttacttattgcaacaattggtgtttcgtgctttcatttgtagGTACAAACTGATCTCCAGTTTATAAAAGAGGACATTAATGCTGTGGAGAAACATAGAATGGATTTGTATCGTGCACGGGACAGGTACTCTGTAAAATTAC
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------tctatcca-actattcatgagacgtataacccctgaatgttagatgagatctcagaatattatagaattctgtcatttatgtcttctctatcttaatgtagGTGCAAACTGATCTCCAGTATATTAAAGAAGATATAAATGCCGTTGAGAGACATAGAATAGATTTATACCGAGCTAGGGACAGATATTCTGTAAAGTTGC
||| | | || | | | ||| |||| | || | | |||| | ||| | | | | | ||| | | | ||||||| |||||||||||||| | ||| ||||| || |||||||| || |||| ||||||||| || || || || || ||||||| || |||||||| ||||
gtgtgcttgctgcaatctctctctccctctactctaaattattgctaagtagctaatgttttccatttttttttctttcctctgtttgcagtagttggtcattatcttaccactgatttctatgttacatct---gtttttacttattgcaacaaatggtgtttcatactttcatttgtagGTACAAACTGATCTCCACTTTATAAAAGAGGACATAAATGCTGTGGAGAAACATAGAATGGAATTGTATCGTGCACGGGACAGGTACTCTGTAAAATTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatctcagaatattatagaattctgtcatttatgtcttctctatcttaatgtagGTGCAAACTGATCTCCAGTATATTAAAGAAGATATAAATGCCGTTGAGAGACATAGAATAGATTTATACCGAGCTAGGGACAGATATTCTGTAAAGTTGC
tcttaat putative branch site (score: 3)
tgtcttctctatctt CT-rich tract
agaatattatagaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatccaactattcatgagacgtataacccctgaatgttagatgagatctcagaatattatagaattctgtcatttatgtcttctctatcttaatgtagGTGCAAACTGATCTCCAGTATATTAAAGAAGATATAAATGCCGTTGAGAGACATAGAATAGATTTATACCGAGCTAGGGACAGATATTCTGTAAAGTTGC
- - -ccaacta
- - - - - - - - - - - - - aacccct
- - - - - - - - - - - - - - - - - - - - - - - -atctcag