Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacaattctcattgtgggaatcaaattttgatgttttgatgataaagcttagcaattttgttaatgcagACTCGAGTTGATCCATCAAGAGACATTATTTATGTTAATGGAAATCGTATTCCTAAGAAACTTCCTCCAAAGGTTTATTTTGCTCTGAACAAGCCTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g05806.1 (Oryza sativa), 3'ss of exon 2
----------------------------gtaaaacaattctcattgtgggaatcaaattttgatgttttgatgataaagctta-gcaattttgttaatgcagACTCGAGTTGATCCATCAAGAGACATTATTTATGTTAATGGAAATCGTATTCCTAAGAAACTTCCTCCAAAGGTTTATTTTGCTCTGAACAAGCCTAAAG
|| ||| | | | | | | | || | || | || || | |||| || | || || ||| |||| |||||| |||| || ||| |||||||||||||| || ||| | ||||| |||||||| ||| | ||||||||| | |||||||| ||||
ggtcattttactatgaattttgatccatgtgcttcaaatgtattcatagaca--agtttattatttgttacatatgattcttatacattcttttttatgtagACCAAAGTTGACATCTCAAAGGATTCTATCTATGTTAATGGAAACCGCATTTCCAAGAAGCTTCCTCCGAAGTTATATTTTGCTGTTAACAAGCCAAAAG
upper sequence: AT2G39140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g04740.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------gtaaaacaattctcattgtgggaatcaaattttgatgttttgatgataaagcttagcaattttgttaatgcagACTCGAGTTGATCCATCAAGAGACATTATTTATGTTAATGGAAATCGTATTCCTAAGAAACTTCCTCCAAAGGTTTATTTTGCTCTGAACAAGCCTAAAG
| |||| ||| ||| | | | | | | | ||| || | | | |||||||||||||||||||||||| | || || || ||||||||||||||||| || |||| ||||| || ||||| ||||| ||| |||| ||||| ||||| ||||
cttagtgttgtagttattgccaaggaagatttgaaactatttctatt-tacatccagagtcataccttagtcttaatagagtt--gtttctgatttaatgcagACTCGAGTTGATCCAGCCAGGGATATGATTTATGTTAATGGAAACCGCCTTCCGAAGAAGCTCCCTCCTAAGGTGTATCTTGCCCTGAATAAGCCAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggaatcaaattttgatgttttgatgataaagcttagcaattttgttaatgcagACTCGAGTTGATCCATCAAGAGACATTATTTATGTTAATGGAAATCGTATTCCTAAGAAACTTCCTCCAAAGGTTTATTTTGCTCTGAACAAGCCTAAAG
tgttaat putative branch site (score: 3)
ttttgtt CT-rich tract
aaattttgatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacaattctcattgtgggaatcaaattttgatgttttgatgataaagcttagcaattttgttaatgcagACTCGAGTTGATCCATCAAGAGACATTATTTATGTTAATGGAAATCGTATTCCTAAGAAACTTCCTCCAAAGGTTTATTTTGCTCTGAACAAGCCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA