Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgggcagtctttcttttgatcagtaatagttaaaattttaagtaaggaatgtatctgtttttttctattcattaaattatcataatttttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTGCCTCGGAAGTCGGGAATAGGCTATGCTGCTAGATACGAGACAGATAAAA

Basic information

species Arabidopsis thaliana
transcript AT3G20000.1
intron # 6
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|124709524|gb|EH800926.1|EH800926
EST:     CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTA
genomic: CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTA
EST: gi|125267639|gb|EL281724.1|EL281724
EST:     CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTATCCTTGGGTGGTGA
genomic: CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGA
EST: gi|47829613|gb|CK119297.1|CK119297
EST:     CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
genomic: CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
EST: gi|86035206|gb|DR330959.1|DR330959
EST:     CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTTCTGGGCTGGTGT
genomic: CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTT-CTGGGCTGGTGT
EST: gi|86035207|gb|DR330960.1|DR330960
EST:     CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
genomic: CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
EST: gi|86035215|gb|DR330968.1|DR330968
EST:     TCAGCTTCAACCTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
genomic: TCAGCTTCAAC-TTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
EST: gi|125021457|gb|EL093726.1|EL093726
EST:     AGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
genomic: AGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTG
EST: gi|86035199|gb|DR330952.1|DR330952
EST:     CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAG                         AGTGTTACAAACCATTTATCCTT
genomic: CTCAGCTTCAACTTGGACAGAGTGCCCTAATTGGAGCAACTTATATCCAGgtaagtttga ... ttttgtacagAGTGTTACAAACCATTTATCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggaatgtatctgtttttttctattcattaaattatcataatttttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTGCCTCGGAAGTCGGGAATAGGCTATGCTGCTAGATACGAGACAGATAAAA
                                          tttttttgt  CT-rich tract
              tttttttctattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgggcagtctttcttttgatcagtaatagttaaaattttaagtaaggaatgtatctgtttttttctattcattaaattatcataatttttttgtacagAGTGTTACAAACCATTTATCCTTGGGTGGTGAAATTTTCTGGGCTGGTGTGCCTCGGAAGTCGGGAATAGGCTATGCTGCTAGATACGAGACAGATAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcataa