Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaacccactatacacacatgcactacttttcatcactggaacacaaactcagtctctaagttgtctttcttttaattagATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35940.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g06340.1 (Oryza sativa), 3'ss of exon 3
-------gtaagtaacccactatacacaca------tgcactact-tttcatcactggaacacaaactcagtctctaag--ttgtctttcttttaattagATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG---------------------------------------
| | | | | || | || || | | | |||| || || | ||| || || | || | | | |||||||| ||||||||||||||| |||||| || |||||||| || ||||| | ||||||
gatcaagctgcattttcgagtgcacgctcaaatcggtgaatgaatatttcctcgtgtcgacgtctcattggtcgctgagattcgttgtgacgtcatgcagATACCCCAAGGATTCGGACAAGGTCATGCTCGCCAAGCAAACCGGCCTCACCAGGAGCCAGGTACGTACGTATACGTCTACGTACAATACTACGTCTACG
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g06340.2 (Oryza sativa), 3'ss of exon 3
-------gtaagtaacccactatacacaca------tgcactact-tttcatcactggaacacaaactcagtctctaag--ttgtctttcttttaattagATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
| | | | | || | || || | | | |||| || || | ||| || || | || | | | |||||||| ||||||||||||||| |||||| || |||||||| || ||||| | ||||||
gatcaagctgcattttcgagtgcacgctcaaatcggtgaatgaatatttcctcgtgtcgacgtctcattggtcgctgagattcgttgtgacgtcatgcagATACCCCAAGGATTCGGACAAGGTCATGCTCGCCAAGCAAACCGGCCTCACCAGGAGCCAG
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G458728_T07 (Zea mays), 3'ss of exon 3
---------------gtaagtaacccactatacacacatgcactacttttcatcactggaacacaaactcagtctcta--agttgtctttcttttaattagATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
|| | | || || || | || | ||||| | | | ||| | | | | | | |||||||| ||||||||||||||| |||||| || |||||||| || ||||| | || |||
tgcttgcttgctttcgtgcccatggcgtcatgcatgcaacccct-cacctcatcgtgtccgcctctaattggtccgcatggatccttgtctcgtcacgcagATACCCCAAGGATTCGGACAAGATCATGCTCGCCAAGCAAACCGGGCTCACCAGGAGTCAG
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G38690.1 (Glycine max), 3'ss of exon 6
----------gtaagtaacccactatacacacatgcactact--tttcatcact----ggaacacaaactcagtctctaagttgtctttcttttaattagATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
|||| | | || | | | |||| | || || ||| | | | || || | || | || || ||||||||||||||||||||||||||||| || |||||||| || ||| | ||||||
gtcttgacgaaaaagttaacaacatttgagttgttgactattaattatattactttatatattatgcatgttgtgctgaaataactgagtttggtttcagTTATCCTAAGGATTCGGACAAGCACATGCTAGCAAAACAAACAGGGCTAACTAGGAGCCAG
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G36070.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------gtaagtaacccactatacacacatgcactacttttcatc--actggaacacaa-actcagtct-ctaagttgtctttcttttaatt--agATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
| || | || | | | |||| || || | | || | || || | | || | | |||| ||| ||| || || |||||||||||||||||||||||||| || || |||||||| | || | ||||||
gtaagcacacttacatttataaaagttctctctttttattttattctcttgtaagtaattatggaaaaagtttacaacattttaaatgtttactgttaatttaattcaaagataatacatgttgtgctgaaataactttgtttggatttcagTTATCCTAAGGATTCGGACAAGCACATGCTTGCAAAACAAACAGGGTTAACAAGGAGCCAG
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtaacccactatacacacatgcactacttttcatcactggaacaca---aactcagtctctaagttgtctttcttttaatt-agATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
|||| | || | || | || ||||| | | | || | |||| || || | | || || | || || || ||||||||||| |||||||||||||| || || |||||||| ||||| || || |||
----gtaagc-acctttcaattttattttatttttccccttcaaagcccagtaattccagttgctgagatattttggttgtgtttcagTTATCCTAAGGATTCAGACAAGCACATGCTCGCCAAACAAACAGGGCTCACCCGGAGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttcatcactggaacacaaactcagtctctaagttgtctttcttttaattagATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
ttgtctttctttt CT-rich tract
tctttcttttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaacccactatacacacatgcactacttttcatcactggaacacaaactcagtctctaagttgtctttcttttaattagATACCCTAAGGATTCGGACAAGCACATGCTAGCTAAGCAAACAGGACTCACTCGTAGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA