Sequence
atgc intronic sequence ATGC exonic sequence...ataatatgttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30470.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 1
ataatatgttgggacgttattcatattctacaa--tattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
| | | | ||| |||| | || | | | | | | || | || ||| ||||| | ||||| || ||||| | || || || | ||||||||||| || |||||||||||||||||||| ||||| || |||||||| |||||| || ||| |||
-tttttaacaaaaaattcatttgggagacacaagtgaaattattagtatactatggga-acatctctacctaacccgcctaactttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA
upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G806347_T01 (Zea mays), 3'ss of exon 1
---ataatatgttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
|| | | | || || | | | | |||| | || || | | | | || || || | ||| ||| ||||| || ||||| |||| ||||| | ||| ||||| || || |||||||| ||||||||||||||||| || |||||||| ||||| | ||||| |||
actgcaaatagcttgaac--catggaggcctttcgtttttttcttcctcatttattgttaaagagaggttcttaactgtgctaacttagtgattttttt-cagGTGGATACAATTCTGGACAAAGAAAATTTTACATTGGAAGAACTTCTTGATGAGGATGAAATTATTCAGGAGTGCAAAGCACTGAACTCAAGACTCATAA
upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G096107_T01 (Zea mays), 3'ss of exon 2
ataatatgttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
| | | | | | || || | | || | | | || | | ||| | | ||| | | | || ||||| || | |||||||| || || | ||| | || |||||||||||||| ||||||||||| ||||| || |||||||| |||||| || | | |
------------gtgagtgcttgcagtt--cgatgttcatttattttttttc--tcctaagctaca---gttttttaaacattccttttatgtctttcagGTGGATACTATTTTGGACAAGGAAAATTTTAAGTTGGAGGATCTTCTTGATGAGGATGAAATAATTCAGGAGTGCAAAGCACTGAATACCCGCTTAATCA
upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G470292_T01 (Zea mays), 3'ss of exon 1
----ataatatgttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgttt---gcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
||||| || || | | | | | ||| | | | | | | | | | ||||| || || | ||| ||| ||||| || ||||| | || ||||| | ||| ||||| || || |||||||||||||||||||||||||| || |||||||| || || ||||||| |||
gggggcaatattttcggg-gccctgggcggcc------actcggctcgaccccccacaggtacggccctgtcttaattctgttaacttagtgctttattttttccagGTGGATACAATTCTTGACAAAGAAAATTTTACATTGGAAGAACTTCTTGACGAGGATGAAATTATTCAGGAGTGCAAAGCACTTAACTCACGACTCATAA
upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G000039_T01 (Zea mays), 3'ss of exon 2
ataatatgttgggacgtta-ttcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
|| | | | | || | || || | || | | | | ||| || | ||| | |||||| | | ||| |||||||| | |||||||| || || | ||| | || || ||||||||| ||||||||||| ||||| || |||||||| |||||| || | | |
---------------gtgagtgcttgcacttcgatgttcatgttttccctcctaaggtacaat--tatttgttaactgcacatttcgttatctcttt-cagGTTGATACTATTTTGGACAAGGAAAATTTTAAGTTGGAATGTCTTCTTGATGAGGATGAAATAATTCAGGAGTGCAAAGCACTGAATACCCGCTTAATCA
upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
--------ataatatgttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgt-ttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
| |||| ||| | | ||| | || || ||| | || | | | | | | || | | || ||| |||| | | || | |||||||| ||| | ||||||||||| || | ||| || || || || || ||||| ||||||||||||||||| ||||||||||| || || | || || |||
gggggactagaataggttag--tttaatttaatttttaaaatgatatg-tagatacgtat------tggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------------ataatatg--ttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
|| | | |||| || ||| | | |||||| | | | | | | |||| || | |||| | ||| || | | | |||| |||||| || | |||||||| || || | |||||| || ||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| || || | |
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgtt-gcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
ttttgttt CT-rich tract
aaatttcgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataatatgttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG