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

gtaagattgcatatgtttccattttcttacttaaatcatttagattagcatttctaagcattattgactgatcttgaatgccatcatcgccttacttggttttattgtatgattttcgttctgttagGCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAACTGGAGTCGATGAAGGAACAAGTAGAGCCCTTAAGAACTTGG

Basic information

species Arabidopsis thaliana
transcript AT1G05060.1
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|116475903|gb|EG518495.1|EG518495
EST:     CAGCCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCGTAAT                         GCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAACTGGAG
genomic: CAGCCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCGTAATgtaagattgc ... gttctgttagGCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAACTGGAG
EST: gi|125142617|gb|EL179801.1|EL179801
EST:     TGGAACGGCAGCCTCGAAACTTGACATGCGTAAT                         GCTGATGACATAAGAACGAAAGGCAAAAGATCTTTTT
genomic: TGGAACGGCAGCCTCGAAACTTGACATGCGTAATgtaagattgc ... gttctgttagGCTGATGACATAAGAACGAAAGGCAAA-GATCTTTTT
EST: gi|164130981|gb|EL988003.1|EL988003
EST:     CAGCCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCATAAT                         GCTGATGACATAAGGACGAAAGGCAAAGATCTTTTTCAGCCAAAAC
genomic: CAGCCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCGTAATgtaagattgc ... gttctgttagGCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAAC
EST: gi|125133281|gb|EL174845.1|EL174845
EST:     CCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCGTAAT                         GCTGATGACATAAGAACGAAAGGCAAAGATTCTTTTTCAG
genomic: CCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCGTAATgtaagattgc ... gttctgttagGCTGATGACATAAGAACGAAAGGCAAAGAT-CTTTTTCAG
EST: gi|86080231|gb|DR375988.1|DR375988
EST:     CAGCCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCGTAAT                         GCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAACTGGAG
genomic: CAGCCACTTTGGTTTTTGGAACGGCAGCCTCGAAACTTGACATGCGTAATgtaagattgc ... gttctgttagGCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAACTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaatgccatcatcgccttacttggttttattgtatgattttcgttctgttagGCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAACTGGAGTCGATGAAGGAACAAGTAGAGCCCTTAAGAACTTGG
                gccttac  putative branch site (score: 3)
                                        ttttcgttct  putative PPT
                           ttttattgtatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattgcatatgtttccattttcttacttaaatcatttagattagcatttctaagcattattgactgatcttgaatgccatcatcgccttacttggttttattgtatgattttcgttctgttagGCTGATGACATAAGAACGAAAGGCAAAGATCTTTTTCAGCCAAAACTGGAGTCGATGAAGGAACAAGTAGAGCCCTTAAGAACTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC