Sequence
atgc intronic sequence ATGC exonic sequencegtaagactcgaaaatcaagactgtatgacctaatcgaatctaaagccactcgatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03910.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 9
-------------------------gtaagactcgaaaatcaagactgtatgac---ctaatcgaatctaaagccactcgatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
| | | || | || | |||| | | | | | | | || || ||| | | | || | | ||| ||||||| || || ||||||||||| ||||| |||||||| | ||||| |||||||||||||| || ||||||| || |||| || ||||| || |
gtaagttactgcacaatctccctgtgctaaattcagag--taaaaatgtaaagcagtcaggttaagcaagagactgatgcatgaagctgctgctgt-tcttgtggtt-tgttcagAACATTCAGGGTTTCATGTGGGACGAGGAGAAGGTGAACAATGAGCTGAAGACCTACATGACCCGTGGGTTCAGGGATGTGAAGGAGATGTGCAGGAGCC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 8
-----gtaa-gactcgaaaatcaagactgtatgacctaatcgaatctaaagccactcgatcaaaaca-ctgatttgtg-ttatatctgtgtga-----agAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
|| | || ||| || ||| ||||| | | | | || | | | | | | || ||||| | ||| | ||||||| ||||| ||||||||||||||||| |||||||| | ||||||||||| ||||||||| ||||||||||| |||| || ||||| | || |
tcactttagtggttccaaattcttttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 9
------------gtaagactcg---aaaatcaagactgtatgacctaatcgaatctaaagccactc-gatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
| | || | | | | | | | | | | | || ||| || | | | || | |||| | |||| | || ||||||| ||||| ||||||||||||||||| |||||||| | ||||||||||| |||||||| ||||||||||| |||| |||||||| | || |
tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgtaa--tcattaaggttaattaaatgatgattattatgta-atgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 9
--------------gtaagactcgaaaatcaagactgtatgacctaatcgaatctaaagcc--actcgatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
| || | | | || | |||| | |||| | | | || | | ||| || || ||| | | ||||||| ||||| ||||||||||||||||| || ||||| | |||||||||||||||||||| || |||||||| |||| |||||||| | || |
aaattgctcattttagaggaattgca--tccttattgtacaaattaattaattaatataccctatgtagcccttaca-tggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 8
--------------gtaagactcgaaaatcaagactgtatgacctaatcgaat--ctaaagccactcgatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
| || | | | | ||||| |||| | | | ||| || ||| || || ||| | | | ||||||| ||||| ||||||||||||||||| || ||||| | |||||||||||||||||||| || |||||||| |||| |||||||| | || |
aaattgctcattttagaggaattgcacccctg--ctgtacaggttaattaattaatatactccatgtagtccttaca-tggttggtgattttgtggcacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcgaatctaaagccactcgatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
cactgat putative branch site (score: 3)
tgttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagactcgaaaatcaagactgtatgacctaatcgaatctaaagccactcgatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA