Sequence
atgc intronic sequence ATGC exonic sequence...aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03940.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
--aaatgtggtttgcgaggccatgccaatggg--tttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
|| | | | | || | || | ||| |||| | | | ||||||| | ||| || || || | | | || || | | || | ||||| || |||||||| | |||| || || |||||| | ||||||||||| |||||||||||||||||||| |||||||| |||||| | |
aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaag-catctaatgt---tttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 2
--aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgattt-cgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
||| |||||| | || || || || ||| || | | | || | || | || | | | | | |||| ||||| || ||||||| || ||| ||| |||| | || |||||||| ||||| || |||||||||||||||||||| |||||| | ||
tagaatacggtttgtttga--gtgtcatctggcacaa-tattgttttacactatgatgagttggagatttggttacctagtaaagtcgatgaatcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAAGGTGGTTTTGGACAGGTTTATGTTGGCAGAAGGGTTTCTGGTGGAACTG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 2
-----------aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
| ||| ||| | | | ||| || | ||| || ||| | || | || | ||||| | || || | |||||||||| || || |||||| | ||||||| ||||||||| | ||||| ||||| ||||||||||||||||||||| | ||| | ||||||||| ||
attccagactgcattgtagttgttgttttta-gttaatatagatagatttggcagtaccttacttaccttatctgtggtgtatattt-------tctcattg---atgcagGTACAAGTAGGTAACTCTCCTATATATAAGATAGAGAGGAAATTGGGTAAGGGTGGTTTTGGTCAAGTTTATGTTGGCCGGAGGTTAAGTGGTGGCTCTG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 2
aaatgtggtttgcgaggccatgcca--atgggtttaagccttgcactagctttttgttctcctttgaga-----gagatattcactatgatttcgttttctgta-tagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
| || | ||| | | || ||| || || | | || || ||| | || | || | | || ||||| || ||||||||||| || ||||||||| | || |||| || ||||| | ||||| ||||| ||||||||||| ||||||||||||||||| |||||||||| ||
--------tctgaggggctaatggagcatttgttaaaatttttccttcactcgttcttcaacacggattctttcaaagcatctagttgttttctgtttttggttctagGTACAAGTGGGTAATTCTCCTATATACAAGATAGAAAGGAAGTTAGGTAAGGGTGGTTTTGGTCAAGTGTATGTTGGCAGAAGGGTAAGTGGTGGCACTG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 1
aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtat----agGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
||| | | || | | | | || ||| | | | || | | | ||| | || | | || ||||| || |||| |||||||| ||||| || || |||| |||||||||||||| || || |||||||||||||| |||||||| | | | |||||||| |
--gtgtcatggatggacgcagctaactatgatggagtgcggca-tgtcgtgacattattact-atgtgagttgttactgacctccttgtattctgaatgcgcagGTTCAAGTTGGTGGCTCTCCAGTCTACAAGATTGAGAGGAAACTTGGAAAGGGAGGCTTTGGTCAAGTATATGTTGGTCGTCGTCTCAGTGGTGGGGCAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 1
aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
| | ||| || | || | | | || | || |||| |||| | | || |||||||||| |||||| || |||| |||||| ||||| || || ||||| ||||||||||||||||| || || | | | || | ||| |
--------------------------------------gtatgatttttttccattggatgtggatgtaactttgcaatttggtttc-ttttgtttccagATACAAGTTGGTGGTTCTCCGGTCTATAGGACGGATAGGAAGCTGGGGAAAGGAGGCTTTGGTCAAGTTTACGTGGGTCGGAAGTTGGGGCCTGGTGATC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 1
aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
| | ||| | | || | | | || | || |||| || | || |||||||||| |||||| || |||| |||||| ||||| || || ||||| ||||||||||||||||| || || | | | || | ||| |
--------------------------------------gtatgatttttttccatcggatgtggatgtaactttgcaatttggtttctcttgttcc--agATACAAGTTGGTGGTTCTCCGGTCTATAGGACGGATAGGAAGCTGGGGAAAGGAGGCTTTGGTCAAGTTTACGTGGGTCGGAAGTTGGGGCCTGGTGATC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 1
aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
| | |||| | | | | | | | | | | || || || || || |||| ||||||||| |||||||| ||||||| |||||||| ||||| |||||||||||||||||||| ||||| || | ||| | ||||| ||| |
------------------------------gtaagtcctttcgcgaaatacaaaatgt--------gggcaaagctaatacgagtttgtggcttgc--agGTCCAAGTTGGAGGCTCTCCTGTATATAAGATCGAGAGGAAGCTTGGAAAAGGTGGCTTTGGTCAAGTATATGTAGGACGGAGGCTTAGTGGCGGCTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
tttcgttttct CT-rich tract
tatgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - ggtttgc
- - - - - - - - -ccatgcc
- - - - - - - - - - - - - - - - - - ccttgca