Sequence
atgc intronic sequence ATGC exonic sequencegtacaatagagtatgcggaatatgggatattagatgaaggattacttttttccccagtcttccgcccatcttcctttcatttggaatgattttgaatctacattctaataacctctgctctggaacagAGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79830.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 4
gtacaatagagtatgcggaatatgggatattag-atgaaggattacttttttccccagtcttccgcccatcttcctttcatttggaatgattttgaatctacattctaataacctctgctctggaacagAGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAG
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---------------------------aattagcatgtgctactgttccctacttctatttctcaattttttttgtgttgtttgctcctgcatcccattta--tttcattgctgataattgtggaacagAGAAAATCCAATGAGGCAGAAGTTGAGTCTTTGCGAGAGGAATACCATCAGAGAGTTGCAACTCTTGAGAGAAAG
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G43330.1 (Glycine max), 3'ss of exon 6
gtacaatagagtatgcggaatatgggatattagatgaaggattacttttttccccag--tcttccgcccatcttcctttcatttggaatgat-tttgaatctacattctaataacctc--tgctc-------tggaacagAGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAG
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----------------------------------------gttactgttcctccctacttctatttctcttttttcttttctttgctgtgttgcttgttcctgcatcccatttatttcattgctgataattgtggaacagAGAAAATCCAATGAGGCAGAAGTTGAGTCTTTGCGAGAGGAATACCATCAGAGAGTTGCAACTCTTGAGAGAAAG
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 3
gtacaatagagtatgcggaatatgggatattagatgaagga-ttacttttttccccagtcttccgcccatcttcctttcatttggaatgattttgaatctacattctaataacctctgctc-tggaacagAGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAG
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-----------------------------taatgtggagcacttagcccccctctctcatttttactactaatacatacattagtactg-tgatatgattgttttctaactactgagaattgtgtaacagAGAAAATCCAATGAAGCAGAAACTGAGTCTCTGCGAGAGGAATACCATCAAAGAGTAGCAGCTCTTGAAAGGAAGMapped 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|125213581|gb|EL228395.1|EL228395EST: AGGATTTGAAG AGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAG
genomic: AGGATTTGAAGgtacaataga ... tctggaacagAGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcatttggaatgattttgaatctacattctaataacctctgctctggaacagAGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAG
taataac putative branch site (score: 1)
cctctgctct CT-rich tract
attctaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatagagtatgcggaatatgggatattagatgaaggattacttttttccccagtcttccgcccatcttcctttcatttggaatgattttgaatctacattctaataacctctgctctggaacagAGGAAATCTAACGAAGCTGAAGTCGAGTCTTTGCGAGAAGAATACCATCAGAGAGTTGCAACTCTTGAGAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA