Sequence
atgc intronic sequence ATGC exonic sequencegtacttccttttatggcttctggctcatatttagtagtttttgtacatatatcaatgaagtagatcaattagtatttgatagaagagggtttataaaggtttggttattgcgcagGCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGTACCATATTGGTTCATGGACTCTCTAGAGTTGTTCTGGAAATACTTAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G05070.1 (Glycine max), 3'ss of exon 2
gtacttccttttatggcttctggctcatatttagtagtttttgtacatatatcaatgaagtagatcaattagtatttgatagaagagggtttataaaggtttggttattgcgcagGCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGTACCATATTGGTTCATGGACTCTCTAGAGTTGTTCTGGAAATACTTAAGA
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gtaaatcactc-acgaactctcgcacgtgcgt----gcgtgcgtgctt---tcattcactcacatca-tcacttcctaaactcagttgattcgc-----ttt--tcgcttcgcagGCTCGCAAGATCATTGCAATGCTCAGTCAAGATTTTATATTCGACGGCTGCACGATTCTCGTTCACGGATTCTCCCGAGTCGTGCTTCAGATTCTCAAAC
upper sequence: AT1G72340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G45180.1 (Glycine max), 3'ss of exon 2
gtacttccttttatggcttctggctcatatttagtagtttttgtacatatatcaatgaagtagatcaattagtatttgatagaagagggtttataaaggtttggttattgc-gcagGCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGTACCATATTGGTTCATGGACTCTCTAGAGTTGTTCTGGAAATACTTAAGA
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---------------------------------gcaacttcc--aactctcgctgcactctaattttcttttctttcctcactctcttgcccattttcctttctttctttttgcagGCCCGCAAAGTTATTGCAATGTTGAGTCAGGATTTTATATTTGATGGCTGTACAATTTTGGTTCATGGTTTTTCCAGAGTCGTCTTTGAAGTCCTGAAAC
upper sequence: AT1G72340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g00390.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtacttccttttatggcttctggctcatatttagtagttt-----ttgta-catatatcaatga-----agtagatcaattagtatttgatagaagagggtttataaaggtttggt-tattgcgcagGCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGTACCATATTGGTTCATGGACTCTCTAGAGTTGTTCTGGAAATACTTAAGA
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gtatattgattatatatttatttttttccctttttccatggtaataattgtttcactattgtgtcatgttgcaattatccccaatgcaaatattcaaattaagcacaaaaacctttcaacttaccccttatattg-acagGCACGCAGAATCATTGCAATGCTTGGTCAAGATTTTATATTTGATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGAMapped 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|164107628|gb|EL980608.1|EL980608EST: TTTGGGGAAATATCTTGCAAG GCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGT
genomic: TTTGGGGAAATATCTTGCAAGgtacttcctt ... tattgcgcagGCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGT
EST:
gi|164189677|gb|ES024392.1|ES024392EST: AGTCTCGTCTTCTTGAACGTGCTGAGAAATTTGGGGAAATATCTTGCAAG GCTCGTAGGATTATCGCAATGCTTAGTCAAG
genomic: AGTCTCGTCTTCTTGAACGTGCTGAGAAATTTGGGGAAATATCTTGCAAGgtacttcctt ... tattgcgcagGCTCGTAGGATTATCGCAATGCTTAGTCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagatcaattagtatttgatagaagagggtttataaaggtttggttattgcgcagGCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGTACCATATTGGTTCATGGACTCTCTAGAGTTGTTCTGGAAATACTTAAGA
atttgat putative branch site (score: 5)
aattagtatttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttccttttatggcttctggctcatatttagtagtttttgtacatatatcaatgaagtagatcaattagtatttgatagaagagggtttataaaggtttggttattgcgcagGCTCGTAGGATTATCGCAATGCTTAGTCAAGATTTTATATTCGATGGTTGTACCATATTGGTTCATGGACTCTCTAGAGTTGTTCTGGAAATACTTAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA