Sequence
atgc intronic sequence ATGC exonic sequencegtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtatatactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 1
gtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtata--tactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
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-------------------------------------------------gagactcgtaagttatg-gctgaaatattccttgcttcaacattttaggtttttagagttccactgttggcatactaaatttat-agattatgt--tgtttcagCTGGCCAGTGTGCGATTGTTTGATTGCTTTTCATTCCTCTGGATATCCCCTGGAAAAGGCTGAAGCATATGCTGCTTTAAGAAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 1
gtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtat-atactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
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-----------------------------------cacttgcaacatttaag--ttatagctgaactattt--------tatttttgttcaccttttagatgttaagagtcatgctg---ttaa----tttttaaatattgtgttatttcagCTGGCCAATATGTGATTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGCGGCATATGCTACTTTAAGAAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 3
gtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtatatactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
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----------------------------------------acgctacaacatttaagttatacctgaact--attttatttttgttcaccttgtag-atgttaagagt-catgctg---ttaatgttt----aaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 3
gtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtatatactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
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------------------------------------------------tgagactcgtaagctatg-gctgaaatatttcttgcttcaacattttaggtgtttagagt-tgcactgttggcatactaaatttatatattatgttatttcaGCTGGCCAGTGTGCGATTGTTTGATTGCTTTTCATTCCTCCGGATATCCCATGGAAAAGGCTGAAGCATATGCTGCTTTAAGAA-
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 3
gtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtatatactggaatcaaaact-ttaccagact-gtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
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------------------------------------------------tgatttcagctatttataagttgagg-gtgtccttgtaacataatcatgcggtttggtctctg-attgatgtctaatttgttgccatgctcgcttac---ttcagCTGGCCAATATGTGATTGCTTGGTTGCCTTCTATTCATCTGGCTACCCTCTTGAAAAGGCTGAAGCTTATGCTGCTTTGAGAAAMapped 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|116449078|gb|EG491670.1|EG491670EST: ATCTTACATTTTGGGGATAAAGTTATACTTGAAGATCCAATAGAAAG TTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCT
genomic: ATCTTACATTTTGGGGATAAAGTTATACTTGAAGATCCAATAGAAAGgtattctgta ... actctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCT
EST:
gi|116448301|gb|EG490893.1|EG490893EST: ATCTTACATTTTGGGGATAAAGTTATACTTGAAGATCCAATAGAAAG TTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCT
genomic: ATCTTACATTTTGGGGATAAAGTTATACTTGAAGATCCAATAGAAAGgtattctgta ... actctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagtacaaagtatatactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
ctgtttactctttc CT-rich tract
aaagtatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtatatactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA