Sequence
atgc intronic sequence ATGC exonic sequence...ttgtagttttcagcatatatcatacagttagctcctggtgttgggatagcgcttaaaatttgtaatctcatgcttatgtttgtttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23310.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 3
ttgtagttttcagcatatatcatacagttagctcctggtgttgggatagcgcttaaaatttgtaatctcatgctt-------atgtttgtttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
||| || |||||| ||| | ||| | | ||| | | |||| | | ||| ||| || || || || |||| ||||||| || || |||||||| | || || |||| ||||| ||||| |||||||||||||| |||||||| ||||||||||||
----tttttccaatatatat-atatgtcttgctgc--ataaccagatttctcataaagatatttatcagatgatttgttacaattttgcaattctttcttttcatagGTTAGAATCTGCCGGGAGAAGGCCACTGGTCATGTATATGCTATGAAGAAGCTTAAGAAATCAGAGATGCTACGTAGAGGCCAG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 2
--ttgtagttttcagcatatatcatacagttagctcctggtgttgggatag-cgcttaaaatttgtaatctcatgcttatgtttgtttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
|| | || | | | || ||| | || | || ||| | || | | || || || || || || || ||||||| || || |||||||| | || ||| |||| ||||| ||||| |||||||||||||| |||||||| || |||||||||
gattttttcccccatatcttgctgcataaataactctgatttttcataaagatatttatcagatgatttgttgcaattttgca-attctttcttttcat--agGTTAGAATCTGCCGGGAGAAGGCCACTGGCCATGTTTATGCTATGAAGAAGCTTAAGAAATCAGAGATGCTACGAAGAGGCCAG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 2
------------------ttgtagttttcagcatatatcatacagtta-gctcctggtgttg-ggatagcgcttaaaatttgtaatctcatgcttatgtttgt---ttttcctct----tgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
|| | | | | | | | | || ||| ||| | || ||| |||| |||| | | || | |||| ||||| ||| | | |||| || | || | ||||| |||| || |||| ||||| ||||| || ||||||||||| |||||||| || |||||||||
gtatagtataatctacctttattttcattgaagttaaaaaaaaaactatgcttctgatctttcacatatgttacaaaaattgttagataatttgcaactttgcaaattttcttcttcttttgtatagGTCAGAGTCTGCCGAGAGAAAGCAACCGGTCATGTATATGCTATGAAGAAACTTAAGAAATCAGAGATGCTTCGCAGAGGCCAG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 2
----------ttgtagttttca--gcatatatcatacagtta-gctcctggtgttg-ggatagcgcttaaaatttgtaatctcatgcttatgtttg---tttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
| |||||| | | || | | | || ||| ||| | || ||| |||| |||| | | || | |||| ||||| | || | |||| || | || | ||||| ||||| || |||| ||||| ||||| || ||||||||||| |||||||| || |||||||||
gtatagtctgcctttattttcattgaagttaaaaaaaaactatgcttctgatctttcacatatgttacaaaaattgtcagataatttgcaactttgcaattttttccttttttatagGTCAGAGTCTGCCGAGAGAAAACAACTGGTCATGTATATGCTATGAAGAAACTTAAGAAATCAGAGATGCTTCGCAGAGGCCAG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 2
ttgtagttttcagcatatatcataca--gttagctcc---tggtgttgggatagcgcttaaaatt-tgtaatctcatgcttatgtttgtttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
|||| | | || | | || || | | || || || ||| | || | | | || || | | |||| | || | || ||||||| | || |||||||||| ||| ||| |||| ||||| ||||| |||||||||||||| |||||||| || || ||||||
-----gtttgtggaaaattttctgcactgtctgttttctttgatgctgttataacatttcatttaacttgattgcacccct-tgttcttacttttctgttctgtagGTTAGAGTCTGCAGGGAGAAGAAAACCGGCCATGTATATGCCATGAAGAAGCTTAAGAAATCAGAGATGCTTCGAAGGGGCCAG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 2
-ttgtagttttcagcatatatcatacagttagctcctggtgttgggatagcgcttaaaatttgtaat-ctcatgcttat--gtttgtttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
||| | | | ||| | | | | | | | | || | | | | | || ||| | |||| | || || | | | | | ||||| || |||| |||||||| ||| | ||| ||||| ||||||||||| ||||| ||||||||||| || |||||||||
gttgaaatctcgagc-ttttttgt-cgg--aacctttgaagctatattggttcataggtaatgtctttctcaagtaaattaacttatgtcttatgtatgctcagGTGAGATTATGCAGGGAGAAATCAAGTACGACTGTGTATGCTATGAAAAAGCTGAAGAAGTCTGAGATGCTACGAAGAGGCCAG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------ttgtagttttcagcatatatcatacagttagctcctggtgttgggatag---cgcttaaaattt--gtaatctcat----gcttatgtttgtttttcct-cttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
| || || |||| | | ||| || | |||| | | | || | || ||| || | | | | | | || ||||| ||| | || || ||||| |||| | |||||||| |||||||| || ||||| ||||||||||| || |||||||||
gtatgtgtccttagtctgaatctgcattccatattcgactagtttgtttaaatgcacttgaatttgctaaccgtgccaagttcggtcatacttccggttatatgctgtgtgccttttctagcatgtgaaaatgtatttgattaagacatcggggatttgatattagctaatttaagctgatgttgcatgtgacagGTGAGGTTGTGCAGAGAGAAAACAAGTTCTACAGTCTATGCCATGAAAAAACTGAAGAAGTCTGAGATGCTTCGAAGAGGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagcgcttaaaatttgtaatctcatgcttatgtttgtttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
tcttgat putative branch site (score: 4)
cttatgtttgtttttc CT-rich tract
ttaaaatttgtaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtagttttcagcatatatcatacagttagctcctggtgttgggatagcgcttaaaatttgtaatctcatgcttatgtttgtttttcctcttgatgcagGTTAGGATATGTAGGGAGAAGACAACAGGCAATGTCTATGCGATGAAAAAGCTTAAGAAATCTGAGATGCTCCGTAGAGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - -tcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatctca