Sequence
atgc intronic sequence ATGC exonic sequencegtacgtattatttaaggctagtagcatttttgttacttattctatccatagacgtacctcttagttcaatatgacaaaaagcatgacttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G10740.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
gtacgtattatttaaggctagtagcatttttgttacttattctatccatagacgtacctcttagttcaatatgacaaaaagcatgacttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
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--------------------------gtttgagtaagcatcat-ttgataataacgtgttctagtttactcttctagtttgtatgt---------aactcaactaacatctaggaatgttattttacatt-----gcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
gtacgtattatttaaggctagtagcatttttgtta-cttattctatccatagacgtacctcttagttcaatatgacaaaaagcatg-acttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
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-------------------------------gtaagcatagtttgacaataa---tgcattctagttcactcttctagtttgtatgcaactcaactaacatctgggagtgt-tatttttcatt----acatt----gcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 6
gtacgtattatttaaggctagtagcatttttgttacttattctatccatagacgtacctcttagttcaatatgacaaaaagcatgacttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
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-------------------atgatccatcttttttccaatttcttcctcgaatttgtcttt---------atgtcatcaagcgt----tcaaataactt---ccaaatttaatgcaatttttt----atctttcaag--agGTGGCTGTTTTGTTGAAGGACAAACATTAAGAAATGCATTTCGGTGGAAAGATAGTGTTGGACCCTGGGAAGAGAGACCTGGTCACTTTGGTGATGTTTG
upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
gtacgtattatttaaggctagtagcatttttgttacttattctatccatagacgtacctcttagttcaata-----tgacaaaaagcatgacttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
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--------------------------------------catccattcataa---tattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatatt-----gcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTGMapped 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|125080065|gb|EL141807.1|EL141807EST: TTTTTCCTAAATGATGGCCGATATAAAACCCCGTTTCATCCGGTTCCCAG GTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCG
genomic: -TTTTCC-AAATGATGGCCGATATAAAACCCCGTTTCATCCGGTTCCCAGgtacgtatta ... gtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
agctaaa putative branch site (score: 3)
atatttgtgaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtattatttaaggctagtagcatttttgttacttattctatccatagacgtacctcttagttcaatatgacaaaaagcatgacttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA