Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgacagtaacatttatgttttgatatgtaactgtaaaaatctttgcagggcatcaattgagtgatatattttgttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAATACATTGACTTACCATTTCCACAGCTTGCGTTCTTCTTGCAGTTTGCTCCTCT

Basic information

species Arabidopsis thaliana
transcript AT1G52590.1
intron # 3
splice site 3'
intron type U2

Mapped 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|125135869|gb|EL175956.1|EL175956
EST:     GTGTCGTACTAGTCGAAAACGATAG                         GTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAATACATTGACTT
genomic: GTGTCGTACTAGTCGAAAACGATAGgtacattgac ... gttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAATACATTGACTT
EST: gi|125260885|gb|EL274970.1|EL274970
EST:     GGAAGAGCTCCTGACGATATATCGAGTGTCGTACTAGTCGAAAACGATAG                         GTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCA
genomic: GGAAGAGCTCCTGACGATATATCGAGTGTCGTACTAGTCGAAAACGATAGgtacattgac ... gttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCA
EST: gi|124903042|gb|EH977122.1|EH977122
EST:     GGAAGAGCTCCTGACGATATATCGAGTGTCGTACTAGTCGAAAACGATAG                         GTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAAT
genomic: GGAAGAGCTCCTGACGATATATCGAGTGTCGTACTAGTCGAAAACGATAGgtacattgac ... gttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAAT
EST: gi|19797858|gb|AU229504.1|AU229504
EST:     GGAAGAGCTCCTGACGATATATCGAGTGTCGTACTAGTCCAAAACGATAG                         GTCTTACATAAAGTCAGAAGCAGTTTT-AAGATCATGAAATACATTGACTT
genomic: GGAAGAGCTCCTGACGATATATCGAGTGTCGTACTAGTCGAAAACGATAGgtacattgac ... gttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAATACATTGACTT
EST: gi|125302047|gb|EL316132.1|EL316132
EST:     GAAGAGCTCCTGACGATATATTCGAGTGTCGTACTAGTCGAAAACGATAG                         GTCTTACATAAAGTCAGAAGCAGTTTTGAAGAT
genomic: GAAGAGCTCCTGACGATATA-TCGAGTGTCGTACTAGTCGAAAACGATAGgtacattgac ... gttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactgtaaaaatctttgcagggcatcaattgagtgatatattttgttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAATACATTGACTTACCATTTCCACAGCTTGCGTTCTTCTTGCAGTTTGCTCCTCT
 atgtaac  putative branch site (score: 3)
 tattttgttttttc  putative PPT
 tgatatattttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattgacagtaacatttatgttttgatatgtaactgtaaaaatctttgcagggcatcaattgagtgatatattttgttttttcagGTCTTACATAAAGTCAGAAGCAGTTTTGAAGATCATGAAATACATTGACTTACCATTTCCACAGCTTGCGTTCTTCTTGCAGTTTGCTCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC