Sequence
atgc intronic sequence ATGC exonic sequence...cagcttctggattgcggcaagaagtacaactttcttcacacatgtgtttccaaattcatgacttcatatttgtctatttgataatgccgcttttctgcagGATATTCTACGATTTCACGCTGTCTACTGGCCTGCCATGCTAATGTCTGCTGGTCTTGAACTTCCCAAGATGGTGTTTGGCCATGGGTTTCTGACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55400.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G23250.1 (Glycine max), 3'ss of exon 6
-cagcttctggattgcggcaagaagtacaactttctt-cacacatgtgtttccaaattcatgacttcatatttgtctatttgataatgccgcttttctgcagGATATTCTACGATTTCACGCTGTCTACTGGCCTGCCATGCTAATGTCTGCTGGTCTTGAACTTCCCAAGATGGTGTTTGGCCATGGGTTTCTGACAAAG
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gcaacccgtgatatatgtttgtgaatgaatttttatgatatttaagaatagctaaaacattgaatttctatatttct--ttaatgattttgttactctgtagGATATTCTACGCTTCCATGCTGTTTACTGGCCAGCTATGCTAATGTCTGCTGGACTAAGCCTTCCTAAAATGGTATTTGGCCATGGATTCTTGACAAAG
upper sequence: AT3G55400.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G43550.1 (Glycine max), 3'ss of exon 6
cagcttctggattgcggcaagaagtacaactttcttcacac--atgtgtttccaaattcatgacttcatatttgtctatttgataatgccgcttttctgcagGATATTCTACGATTTCACGCTGTCTACTGGCCTGCCATGCTAATGTCTGCTGGTCTTGAACTTCCCAAGATGGTGTTTGGCCATGGGTTTCTGACAAAG
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caacccatgatatatgttagttaatgaattttttatgatatgaaagaatagctaaaacattgattttgtatatttct--ttaatgattttgttactctatagGATATTCTACGCTTCCATGCTGTTTACTGGCCAGCTATGCTAATGTCTGCTGGACTAAGCCTTCCTAAAATGGTATTTGGCCATGGATTCTTGACAAAGMapped 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|116429746|gb|EG472338.1|EG472338EST: AAACTGCTGTTTCATTTGGCTGGCCTGCTTCATTGCATTTGATCGGAAAG GATATTCTACGATTTCACGCTGTCTACTGGCCTGCCATGCTAATGTCTGCT
genomic: AAACTGCTGTTTCATTTGGCTGGCCTGCTTCATTGCATTTGATCGGAAAGgtatagctta ... ttttctgcagGATATTCTACGATTTCACGCTGTCTACTGGCCTGCCATGCTAATGTCTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttccaaattcatgacttcatatttgtctatttgataatgccgcttttctgcagGATATTCTACGATTTCACGCTGTCTACTGGCCTGCCATGCTAATGTCTGCTGGTCTTGAACTTCCCAAGATGGTGTTTGGCCATGGGTTTCTGACAAAG
atttgat putative branch site (score: 5)
ccgcttttct putative PPT
atatttgtctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagcttctggattgcggcaagaagtacaactttcttcacacatgtgtttccaaattcatgacttcatatttgtctatttgataatgccgcttttctgcagGATATTCTACGATTTCACGCTGTCTACTGGCCTGCCATGCTAATGTCTGCTGGTCTTGAACTTCCCAAGATGGTGTTTGGCCATGGGTTTCTGACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG