Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcatttttccttcgtctgtcaagattagcatttcctttgattttatcgtatttcaaagtattgggtagatgacaaaagacatactcatttcggctgaagcagagcattcttattctcatctcactaaagattttgttttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G47750.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G47750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G026065_T01 (Zea mays), 3'ss of exon 2
gtgagtcatttttccttcgtctgtcaagattagcatttcctttgattttatcgtatttcaaagtattgggtagatgacaaaagacatactcatttcggctgaagcagagcattcttattctcatctcactaaagattttgt-tttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGAC
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--------------------------------------------tttctgacctatttataa--actagatttgtgctat------tatctgtcttcattaaaacg----actttaaattatttggcattgattatctaataccttgatgttt--cagGTTCTATGTGGCAGAGGTACTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTTAAACCAGAAAATGTCCTCGTTCGGGAAGAT
upper sequence: AT5G47750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
gtgagtcatttttccttcgtctgtcaagattagcatttcctttgattt--tatcgtatttcaaagtattgggtagatgacaaaagacatactcatttcggctgaagcagagcattcttattctcatctcactaaagattttgttttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGAC
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------------------------------------------tgatttcttttcttgctttgcatttttgggttttt-----------tgcctggtttggcaattatgttatgatttgatggt-atc-cactgctaatttccttgtaactt----gcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
upper sequence: AT5G47750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtcatttttccttcgtctgtcaagattagcatttcctttgattttatcgtatttcaaagtattgggtagatgacaaaagacatactcatttcggctgaagcagagcattcttattctcatctcactaaagattttgttttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGAC
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----------------------------------------------gttattgggggctcaagtcttcaatcagctctgcaagacaaa---atttatctttcacctttgtatttgaa-----atttgattgtaatttttacctttcacctg---cagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGACMapped 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|116456362|gb|EG498954.1|EG498954EST: ACTCTCAGGCAACGCCAGCCGGGGAAACATTTTTCTGAGCAAGCGGTAAA ATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGG
genomic: ACTCTCAGGCAACGCCAGCCGGGGAAACATTTTTCTGAGCAAGCGGTAAAgtgagtcatt ... tgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGG
EST:
gi|164170254|gb|ES036303.1|ES036303EST: CAGGCAACGCCAGCCGGGGAAACATTTTTCTGAGCAAGCGGTAAA ATTTTACATAGCAGAGTCATTGCTAGC
genomic: CAGGCAACGCCAGCCGGGGAAACATTTTTCTGAGCAAGCGGTAAAgtgagtcatt ... tgtgtggcagATTTTACATAGCAGAGTCATTGTTAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcagagcattcttattctcatctcactaaagattttgttttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGAC
cactaaa putative branch site (score: 2)
taaagattttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcatttttccttcgtctgtcaagattagcatttcctttgattttatcgtatttcaaagtattgggtagatgacaaaagacatactcatttcggctgaagcagagcattcttattctcatctcactaaagattttgttttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC