Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39590.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 3
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggat--attctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
| | || | ||| | | | | | | ||| || || || | || | | ||||| | | | | | | | | ||||||| ||||| ||||| ||||| || |||||||| ||||||||||| |||||||| || |||||||| | ||| | || ||||| || ||||
-------------gttagtccaatccgctgtctctataaaagctgattagagtt------gtctgtacaatatgaaaccagtgctaactgtgcctctttgactggt-gtgtagTTTGGCTACATCGTCCTAACAACTTCTGCTGGAATTATGGACCATGAGGAGGCTAGCCGTAAGAATGTTGGTGCCAAGGCTCTAGGTTTCTTTTACTGAA
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G018228_T02 (Zea mays), 3'ss of exon 2
gtaaaaaactaaccattcttttat-ttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattga-gcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
|| | | | | ||| | | | | | |||| || || || | || | | || | || | | || | ||||||| ||||| ||||| ||||| || |||||||| ||||||||||| ||||| | || |||||||| ||||| || || ||||| || || |
--------------gttagtccaggctgctgtctctacaaaatctgattagagttt-----gtctgtacactttg--accccagtgctaactgtgcctctttgactggtgtagTTTGGCTACATCGTCCTAACAACTTCTGCTGGAATTATGGACCATGAGGAGGCCCGCCGTAAGAATGTTGGTGGCAAGGTTCTAGGTTTCTTTTATTGAA
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G00590.1 (Glycine max), 3'ss of exon 2
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttat-tgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
||||| ||| | ||| || | | || | || | || | || | || | | | | | | | | || | |||| |||||||||||| |||||| ||||||| || ||||| |||||||| |||||||||||||||| || |||||||| || |||||| | ||||| |||||||||
---------taacctatctgtgattaaac---tttatgttgtccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
|||||| ||| | ||| || | | || || | || || | || | | | | | | | | || | |||| |||||||||||| |||||| ||||||| || ||||| |||||||| |||||||||||||||| || |||||||| || |||||| | ||||| |||||||||
--------ctaacctatctgtgattaaac---tttatgttgccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G45060.1 (Glycine max), 3'ss of exon 3
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttat-tgtgtttgatcattgtgggatattctaacaaagtatgtgtac-caaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
|||||| ||| | ||| || | | || | || | || | | | || | | | | | ||| | || | | |||| || ||||||||| || |||||| ||||||| || ||||| |||||||| |||||||||||||||| || |||||||| || |||||| | ||||| |||||||||
--------ctaacctatctgtgattaaac---tttatgttgtccgttattctcttgtgcgcatatggtttctcctgtttgcccc--taaactttgattgctcaaaatgcgcagTTTGGTTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 3
gtaaaaaactaaccattcttttat-ttaataaatctctgagaccaattcatggtttattgtgt-ttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
| | |||||||| ||| || ||| | || | || | || || | | | | | ||| | | |||| ||| ||| |||||||||||| ||||| |||| || || ||||| |||||||| |||||||||||||||| |||||||||||| || || || | || || |||||||||
-----agattaaccattgaactatattgatagtttactctgttatgttgaatacaaatggttcctccacctatcccttacattttgatt---tatg-gta----attatgcagTTTGGGTATATTGTATTGACTACCTCTGCTGGCATCATGGATCATGAAGAGGCTAGGAGGAAAAATGTTGGTGGTAAGGTATTGGGCTTCTTCTACTAGT
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G10950.1 (Glycine max), 3'ss of exon 3
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtac-caaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG
| ||| | | | | ||||| | | | | || || | | |||| | | | | ||||| | ||| ||| ||||| |||||||||||| ||||| |||| || |||||||| |||||||| |||||||| ||||||| || |||||||
-------attaagctggtgcctgtatcctaaatttttta-atcatggtataggct-ttgtacacagtttccattgttgaccctaacc---tttgtttacacaaatgttgcagTTTGGGTATATTGTGTTGACTACCTCAGCTGGCATCATGGATCATGAAGAAGCTAGGAGAAAGAATGTTG-----------------------------
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G38520.1 (Glycine max), 3'ss of exon 3
gtaaaaaactaaccattcttttat-ttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
| | |||||||| ||| | || | || | | ||| | || | | || | || || | || | ||| || || |||||||||||| ||||| |||| || || || || |||||||| || ||||| ||||||| ||||||||||| || || || || ||||| |||||||||
-----agattaaccattgaactatactgattggttactctg------ttatgttgaatacaaatggttcctccacttatcccttaccttttgatttatactaatttt-gcagTTTGGGTATATTGTATTGACTACCTCTGCCGGCATCATGGATCACGAAGAAGCTAGGAGAAAAAATGTTGGTGGTAAGGTACTGGGTTTCTTCTACTAGA
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 3
------gtaaaaaactaaccattcttttatttaataaa----------tctctgagaccaattcatggtttattgt----gtttgatcattgtg----ggatattctaacaaagtatgtgtaccaaat----tgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
| ||||| || ||| |||| | || ||| ||| | | || | ||| | || | |||||| | | ||| | | | || || | | | ||||||||| || |||||| ||||||| || ||||| |||||||| |||||||| ||||||| ||||||||||| |||||||| |||||||| || ||||||
gttggcatccaaaacccactattttttttataaaaaaaaaaaaaatgatcttaaaaatgaact--tggcaaactgcaaggggccaatcattattctttgagtatgatttcttggggtgactaatgagtgctatttgcagTTTGGATATATTGTCTTGACAACTTCTGCTGGCATCATGGATCATGAAGAAGCTAGGAGAAAAAATGTTGGTGGCAAAGTTCTTGGTTTCTTTTACTAGT
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 4
---gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
| | | || | | | ||| || || || |||| | ||| ||| || ||||| || || | | || ||||| ||||||||| |||||||| ||||| || || ||||| |||||||| ||||| |||||||||| || |||||||| ||||||||||||||||| |||||||||
tattttagctgcatactagtgtattacaggctagatttcctttgccaac----aatatat-gtggtt--tcatttgatgacctttgatgatggt-------ccaaaaattgcagTTTGGATACATTGTGCTGACTACTTCGGCTGGCATCATGGATCATGAGGAGGCTAGGAGAAAGAATGTTGGTGGCAAAGTGCTTGGTTTCTTCTACTAGG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S41_94V6.2 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatca----ttgtgggatattctaacaaagtatgtgtaccaaatt-----gagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
| | || | || || | | | | | | | | | | || || | || | | | |||| || ||| | ||||| | | || | |||||| || |||||||| |||| || || |||||||||||||| || || || ||||||| ||||||||| || ||||| || | || || || ||||||
gttattatttaccacctgtcatcgtggtctactcaatattattcaaaatcggtggtacaatgtggtgctgtggagatagc--ttaacgcatgtgacggttgcgtcatcctagtacttctctttttttcttcgtttagagtcggtggaatcttcattccttatatgtattttatttttgcctgtgcagTTCGGATACATTGTTTTGACCACTTCGGCTGGAATCATGGATCACGACGAAGCTAGGAGGAAAAATGTCGGAGGCAAGGTTTTGGGATTCTTTTACTAGT
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
|| | || | || | | | | | | | | | | || || || ||| | || || | | ||| | | | ||| |||||||| |||||||| |||| || |||||||| ||||||||||| || |||||||| | ||| |||||||| || || || |||||||| || ||||
---aacgatcaagcgttaatcctcctcaagaggatttcatgtta--ccgctgctt-ttaggtatgaac---ctgaaatctgattgttgagtttttcatcttttttg--cagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAGGCTAGAAGGAAGAATGTTGGAGGAAAGGTCCTTGGTTTCTTTTACTGAG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ26253 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-
||| || | | ||||| ||| |||| || || | | | || |||| | | | | |||||||| |||||||| ||||||||||| |||| |||||||| || || || || |||| ||| |||||||| ||||| || || || || ||||| |
----------------------gtttgat---tttgagagacgaatcgatggcttggtgcaaagaactaacg----attttct-------cttcgatctctggct---cagTTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG
ttctaac putative branch site (score: 1)
atattctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG