Sequence
atgc intronic sequence ATGC exonic sequencegtctctttctttctgaaacaatgatccttataatgttcccctattgtccctgtatataaatacttattatcctttcttgatttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20630.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA12G22240.1 (Glycine max), 3'ss of exon 14
gtctctttctttctgaaacaatgatccttataatgttcccctattgtccctgtatataaat-acttattatcctttcttgatttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
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-------------gtatgttatg-tctttata-----tgcctattaacgttaaaaaggtattatatattttgttaagcatttttcttctttcagATGTGTACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA06G39770.1 (Glycine max), 3'ss of exon 14
gtctctttctttctgaaacaatgatccttataatgttcccctattgtccctgtatataaatacttattatcctttcttga-----tttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
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gtatgttttgtctttatatgcctattaatgttaaaaagtattatattttaaagatttttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv19s0014g03910.t01 (Vitis vinifera), 3'ss of exon 2
gtctctttctttctgaaacaatgatccttataatgtt-cccctattgtccctg---tatataaatacttattatc---------ctttcttgatttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
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-----cctccttgcaaagcaaattttttaacattattacttttgttttacttgaaatgtgcaattattaattattaccacgtttttatcatatttgactgtc-cagATGTCTACATAGATGTTCCTGATATCATTGATATTAGTCACATGCGTAGCAGGGGCATTCAGCCTGGGGAAGAGCTATTACCAGAGGCTG
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv03s0017g00960.t01 (Vitis vinifera), 3'ss of exon 2
gtctctttctttctgaaacaatgatccttataatgttcccctattgtccctgtatataaatacttattatcctttcttgatttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
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------------------------------------------gtatctttcatacaggactgttggtc-taacttcatatttgactgtc-cagATGTCTACATAGATGTTCCTGATATCATTGATATTAGTCACATGCGTAGCAAGGGCATTCAGCCTGGGGAAGGGCTATTACCAGAGGCTG
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv19s0014g03920.t01 (Vitis vinifera), 3'ss of exon 15
-------------------gtctctttctttctgaaacaatgatccttataatgtt-cccctattgtccctg---tatataaatacttattatcctt---------tcttgatttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
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gtatctttcatgtgcctttatttgcctccttgcaaagcaatttttttaacattattacttttgttttacttgaaatgtgcaattattaattattactacgtttttatcatatttgactgtc-cagATGTCTACATAGATGTTCCTGATATCATTGATATTAGTCACATGCGTAGCAGGGGCATTCAGCCTGGGGAAGAGCTATTACCAGAGGCTGMapped 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|164230928|gb|ES011758.1|ES011758EST: CATGCGGAAATTTGTTATGGAGGAAGGCTGGGTGCCAAAGAAACTTG ATGTATACATTGATGTTCCG
genomic: CATGCGGAAATTTGTTATGGAGGAAGGCTGGGTGCCAAAGAAACTTGgtctctttct ... actgtggcagATGTATACATTGATGTTCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctattgtccctgtatataaatacttattatcctttcttgatttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
tcttgat putative branch site (score: 4)
tatataaatacttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctttctttctgaaacaatgatccttataatgttcccctattgtccctgtatataaatacttattatcctttcttgatttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG