Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatagttttcttattgaatacttttctctgtctgaggtaatacgtaagtaacaatgttaattgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 3
gtgagtatagtt-ttcttattgaatacttttctctgtctgaggtaatacg-taagtaacaatgttaattgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
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gtcagccaatttactgttcctcgacttgccattctgt-tgttgccgtgcactggatggtaaaactaacactatttatcttacgcctttcagAATGAGACTCAGGACTTCCTTTTCATTGCGACTGAAAGATACAAATTCTGTGTTCTGCAGTGGGATGGAGAAAAATCGGAGCTTCTCACTAG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g51480.2 (Oryza sativa), 3'ss of exon 3
gtgagtatagttttcttattgaatacttttctctgtctgaggtaatacgtaagtaacaatgttaattgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
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-------------------------------------------------------gtaaaactaacactatttatcttacgcctttcagaatgagactcaggacttccttttcattgcgactgaaagatacaaattctgtgttctgcagTGGGATGGAGAAAAATCGGAGCTTCTCACTAG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
-----------gtgagtatagttttcttattgaatacttttctctgtc-tgaggtaatacgtaagtaaca-atgttaattgatagcacttcatctttt---gcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
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gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
----------gtgagtatagttttcttattgaatacttttctctgtctgaggtaatacgtaagtaacaatgttaattgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
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gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttt-tttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtatagttttcttat---tgaatacttttctctgt----ctgaggtaatacgtaa-gtaacaatgttaattgatagcacttcatcttttg-cagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
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gtaagtatcatcttgtgacatatagaaagcttacttagtagcattataatcatgctttttatgctaatactattgcttgctgttttggattctaacagGGCGAAGCACAAGATTTTCTATTCATCGCAACTGAAAGATACAAGTTTTGTGTTCTTCAATGGGATGCAGAGAATTCTGAGGTTATTACAAG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 3
-----gtgagtatagttttct-tattgaatacttttctc-tgtctgag---gtaatacgtaagtaacaatgttaa-ttgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
| | || || || || ||| | || | ||| ||| | || | ||| | || || || | | | | | || |||||||| |||||||| | | ||| | | |||||||||||||| |||||||||||||||||| || || | ||||||| |
ggttccttatcgtacttgtcaacatggaactcagcgctagcatatgaacttataaaaaatatgacgcaacgaaaactttattgttgtgcttttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctgaggtaatacgtaagtaacaatgttaattgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
cttcatctttt CT-rich tract
taacaatgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatagttttcttattgaatacttttctctgtctgaggtaatacgtaagtaacaatgttaattgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT