Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatatatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05420.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 3
----gtgagtata-tatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtatt-gtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
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gtcagccaatttactgttcctcgacttgccattctgttgttgccgtg-cactggatggtaaaactaacactatttatcttacgcctttc--agAATGAGACTCAGGACTTCCTTTTCATTGCGACTGAAAGATACAAATTCTGTGTTCTGCAGTGGGATGGAGAAAAATCGGAGCTTCTCACTAG
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g51480.2 (Oryza sativa), 3'ss of exon 3
gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtatt-gtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
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----------------------------------------------------gtaaaactaacactatttatcttacgcctttc--agaatgagactcaggacttccttttcattgcgactgaaagatacaaattctgtgttctgcagTGGGATGGAGAAAAATCGGAGCTTCTCACTAG
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 3
----gtgagtatatatctcttat-tgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgt----agGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
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gtaagctaatttaaagttcatccatccgagatactttatttgtttttgtgaagtatttttataaatggattttttctgtttgtttcttatcctcagAATGAGACTCAGGACTTTCTTTTCATTGCTACGGAGAGGTACAAATTCTGTGTTCTGCAATGGGATGCAGAAAAGTCAGAGCTAATCACCAG
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
-------------gtgagtatatatctctta--ttgtgttcttttgtcatggtcttaataatgagttaaa-atgttgatagtattgtccaccgtctttt---gtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
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gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgt-ttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
--gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatg-agttaaaatgttgatagtattgtccaccgtcttttgt----------agGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
| || || | | |||| || || || || |||| ||| || |||| | ||| | | | | |||| | |||| |||||||| || | | | || ||||||||||| |||||||||||||||||||||||||||||| | ||| | ||||||| ||||| |
gtgagaaaattcaagcatccttgt-tttttgagttattgtct-aatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtatatatctcttattgtgt-------tcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtctt------ttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
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gtaagtat-catcttgtgacatatagaaagcttacttagtagcattataatcatgcttttta-tgctaatactattgcttgctgttttggattctaacagGGCGAAGCACAAGATTTTCTATTCATCGCAACTGAAAGATACAAGTTTTGTGTTCTTCAATGGGATGCAGAGAATTCTGAGGTTATTACAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116483004|gb|EG525596.1|EG525596EST: ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCAT GGCGAAGCGCAAGACCTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
genomic: ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCATgtgagtatat ... tcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
ccgtctttt CT-rich tract
ttaataatgagttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT