Sequence
atgc intronic sequence ATGC exonic sequencegtaattttgttcatctcctcagaatcttttaaattatcatatttgtggataatgatgtgttagtttaggaattttcctactaaaggtaatctcttttgaggacaagtcttgtttttagcttagaaatgatgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51820.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 3
gtaattttgttcatctcctcagaatcttttaaattatcatatttgtggataatgatgtgttagtttaggaattttcctactaaaggtaatctcttttgaggacaagtcttgtttttagcttagaaatgatgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG
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-------------------------------------------------------------agcatggatacctctttaac-----------cttttgcaatctagccatttgt---gtctaaaactg----gaaactatgcaatattaatcaat----gtcctctttcatatggcg-gcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG
upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 3
gtaattttgttcatctcctcagaatcttttaaattatcatatttgtggataatgatgtgttagtttaggaattttcctactaaaggtaatctcttttgaggacaagtcttgtttttagcttagaaatgatgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG
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----------------------------------------------------------------ttatgcagttaccagataactgtaa---------------aataatgcatttatcagataactgtttttgaaaagt-atttgtatttcataattgattgggtaatatatggtg----cagAATAAGTGGAAGATTCGTCTTCAACTTACAAAGCCAGTCACTTGGCCTCCATTAGTTTGGGGTGTAGTTTGTGGAGCTGCTGCTTCTG
upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 3
gtaattttgttcatctcctcagaatcttttaaattatcatatttgtggataatgatgtgttagtttaggaattttcctactaaaggtaatctcttttgaggacaagtcttgtttttagcttagaaatgatgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG
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-----------------------------------------------------------------tatgcagttaccagataactgtaaattaatgcagttattagataacttttt--tttaaaaa-------aatattgtgtttcttaattga------ttgggtaatatatggtg----cagAATAAATGGAAGATTCGTCTTCAACTCACAAAGCCTGTCACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGG
upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 3
gtaattttgttcatctcctcagaatcttttaaattatcatatttgtggataatgatgtgttagtttaggaattttcctactaaaggtaatctcttttgaggacaagtcttgtttttagcttagaaatgatgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG
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---------------------------------------------------------------------------cagtttggaggtgtttttttttattagaaagacat----ttagc---agaattatatgaagattaaaatctgcaactagagttgattgtatgatttgtattgtg--cagAATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGMapped 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|124918678|gb|EH992495.1|EH992495EST: GTTCAAGCATTAACCAGCTTCTCGGTATCAAAGGAGCATCTCAAGAAACT AATAAATGGAAGATTCGT
genomic: GTTCAAGCATTAACCAGCTTCTCGGTATCAAAGGAGCATCTCAAGAAACTgtaattttgt ... ctgtattcagAATAAATGGAAGATTCGT
EST:
gi|125244480|gb|EL258565.1|EL258565EST: GTTCAAGCATTAACCAGCTTCTCGGTATCAAAGGAGCATCTCAAGAAACT AATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCA
genomic: GTTCAAGCATTAACCAGCTTCTCGGTATCAAAGGAGCATCTCAAGAAACTgtaattttgt ... ctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG
agctaaa putative branch site (score: 3)
tttgttgttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttgttcatctcctcagaatcttttaaattatcatatttgtggataatgatgtgttagtttaggaattttcctactaaaggtaatctcttttgaggacaagtcttgtttttagcttagaaatgatgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT