Sequence
atgc intronic sequence ATGC exonic sequencegtaagctccaaagttccacatttttgatctttggcccttcaaaaaagtttggtgttttgagtcttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14770.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 5
-----gtaagctccaaagttccacatttt-tgatctttggcccttcaaaaaagtttggtgttttgagtcttctgatg---------tttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
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agggagaagggatctgtgttctatttctggcaaactgtctttacactgatacattgtctgatttctgttacatgataaatttttgcttaatttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G322090_T01 (Zea mays), 3'ss of exon 6
-----gtaagctccaaagttccacatttttgatct---ttggcccttcaaaaaagtttggtgttt------tgagtcttctgatgtttg-tgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
| | || ||| | | || || | || | | || | || | | ||| || | || || | | |||||||||||||| || |||||||||||||||||||| ||||| ||||| ||||| | ||| || || | | ||| || || ||| | ||
gggagaaaggatctgtagtatattcctggcaagctatctttacactgatagattgtctcgtttctgttacatgataatttttttgcttaatttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTCAGAACAACCAGAGTCATATGGAAACAGTTCTGTCTACA
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
----------gtaagctccaaagttccacatttt---tgatctttggcccttcaaaaaagtttggtgttttgagtcttctgat--gtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
| || || || ||| || | | | | || || | || || | | |||| || | | | | |||||| ||||| |||||||||||||||||||| |||||||| || ||| |||| || ||||||||||||||||| |||| || ||| || |||
aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
-------gtaagctccaaagttccacatt-tttgatctttggc------ccttcaaaa-aagtttggtgttttgagtcttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
| || || || ||| |||| ||| | ||| | || || | || || | | || | || | | | |||||| ||||| |||||||||||||||||||| |||||||| || ||| |||| || ||||||||||||||||| |||| || ||| || |||
cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 7
--------------gtaagctccaaagttccacatttttgatctttggcccttcaaaaaagtttggtgttttgagtc--ttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
| ||||| | | | | | ||| || | || | | | | | || | | | | | || |||||| ||||| |||||||||||||| ||||| |||||||| || || || ||| || |||||||| |||||||| ||||||||| ||| || |||
tgtttttattcaatgcaagctttggaaccaaaaaagggaaagaaaatgacct-cactgtatttgaatatacttattttatttttctttctttttgtatcagTTATTGTGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 5
gtaagctccaaagttccacatttt--------tgatctt-tggcccttcaaaaaagtttggtgttttgag-----tcttctgatgtttgtgtggtg-cagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
| ||||| | | | | ||| || | || ||| || | || || |||| | | || | | || |||||| || || |||||||||||||| ||||| |||||||| || || || ||| || |||||||| |||||||| ||||||||| ||| || |||
gaaagctttagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttattttctttttcttttctttttgtatcagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
------------------gtaagctccaaagttccacatttttgatctttggcccttcaaaaaagtttggtgttttgagtcttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
| || | | | ||| | | | || | | | || ||||| | | | | | || | | ||||||||||||||||||||||||||||| ||||| || |||||||||||||||| ||| ||||| || |||||||| |||||||| ||| || || |||
tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttga--ccttttaagcttct-tcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggcccttcaaaaaagtttggtgttttgagtcttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
ttctgat putative branch site (score: 3)
aaaaaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctccaaagttccacatttttgatctttggcccttcaaaaaagtttggtgttttgagtcttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA