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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatagcccacacataatataactccccctttctgttacacactctcgtactgaaccgtcttttttataacgtcttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAGAGGAAGAACACCTCCAAG

Basic information

species Arabidopsis thaliana
transcript AT4G32420.1
intron # 12
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|116443354|gb|EG485946.1|EG485946
EST:     TCTCCTGATCGATCTCCTTATCGCTTTAGTGATAGGAGTGACCGTGACAG                         ATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
genomic: TCTCCTGATCGATCTCCTTATCGCTTTAGTGATAGGAGTGACCGTGACAGgtgaatagcc ... ttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
EST: gi|116447362|gb|EG489954.1|EG489954
EST:     TCTCCTGATCGATCTCCTTATCGCTTTAGTGATAGGAGTGACCGTGACAG                         ATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
genomic: TCTCCTGATCGATCTCCTTATCGCTTTAGTGATAGGAGTGACCGTGACAGgtgaatagcc ... ttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
EST: gi|124997114|gb|EL069383.1|EL069383
EST:     TTTAGTGATAGGAGTGACCGTGACAG                         ATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
genomic: TTTAGTGATAGGAGTGACCGTGACAGgtgaatagcc ... ttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
EST: gi|116409463|gb|EG452055.1|EG452055
EST:     TCTCCTGATCGATCTCCTTATCGCTTTAGTGATAGGAGTGACCGTGACAG                         ATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
genomic: TCTCCTGATCGATCTCCTTATCGCTTTAGTGATAGGAGTGACCGTGACAGgtgaatagcc ... ttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
EST: gi|125196340|gb|EL211294.1|EL211294
EST:     GACCGTGACAG                         ATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG
genomic: GACCGTGACAGgtgaatagcc ... ttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgttacacactctcgtactgaaccgtcttttttataacgtcttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAGAGGAAGAACACCTCCAAG
                                   ttataac  putative branch site (score: 2)
                                         cgtcttctct  CT-rich tract
                             tcttttttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatagcccacacataatataactccccctttctgttacacactctcgtactgaaccgtcttttttataacgtcttctctgtagATTTAGAAGTCGCAGAAGGTTCTCGCCAAGTCGGTTCAGAAGCCCACTAAGAGGAAGAACACCTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC