Sequence
atgc intronic sequence ATGC exonic sequence...aactattgaagatttgctggtttcggttcctcaaacataaactatgcacagtatatgcttaagccttgtccccattttaatgtcccattttctgttgtagGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G06130.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G05470.2 (Glycine max), 3'ss of exon 4
aactattgaaga--tttgctggtttcggttcctcaaacataaactatgcacagtatatgcttaagccttgtccccattttaatgtcccatt-ttctgtt-gtagGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
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tgctgctaatgtcttttatttgatttgattttctttacttcaacc-tgc-tgatcctcacttt--ttcaatttactatctaatatctatttgtactataagcagGTCATGTAAGCTTCTACTTTCCAGGTTCTGGGGCAATTTTTACTGGAGACACCTTGTTCAGCTTATCATGTGGCAAGCTCTTAGAAGGAACCCCCGAACA
upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 4
-----aactattgaagatttgc--tggtttcggttcctca-aacataaactatgcacagtatatgcttaa-gccttgtc-cccatttt---aatgtcccatttt------ctgt-tgtagGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
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gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G13470.1 (Glycine max), 3'ss of exon 4
aactattgaagatttgctggtttcggttcctcaaacataa--actatgcacagtatatgcttaagcctt--gtccccattttaatgtcccatt-ttctgtt-gtagGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
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------aaggtgtttgctaatgtcttttatttgattttcataacttcaacctgttgatcctcacttttccaatttactatctaatatctatttgtactataagcagGTCATGTAAGCTTCTACTTTCCGGGTTCTGGGGCAATTTTTACCGGAGACACTTTGTTCAGCTTATCATGTGGCAAGCTCTTAGAAGGAACCCCCAAACA
upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 6
aactattgaagatttgctggtttcggttcctcaaacataaactatgcacagtatatgcttaagccttgtccccattttaatgtcccattttctgttgta----gGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
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--ttatatttggcttctagattcacatagttccccctttttcttttctttattaataatttaacctaattt--aattttgtgtattgattttaattgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAMapped 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|124920450|gb|EH994163.1|EH994163EST: GTTTGCTGGCCATGAAGTCCATATTATGGAAACTCCTGGCCACACCAGAG GCCATATTAGTTTCTACTTTCCAGGGGCACG
genomic: GTTTGCTGGCCATGAAGTCCATATTATGGAAACTCCTGGCCACACCAGAGgttgaatact ... tctgttgtagGCCATATTAGTTTCTACTTTCCAGGGGCACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcacagtatatgcttaagccttgtccccattttaatgtcccattttctgttgtagGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
ttttaat putative branch site (score: 3)
tcccattttctgtt CT-rich tract
attttaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aactattgaagatttgctggtttcggttcctcaaacataaactatgcacagtatatgcttaagccttgtccccattttaatgtcccattttctgttgtagGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA