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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtttctggtttctctcgatagaaattcattagaagcaacaaatatagttaatagatttgctttctgttttctattaatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGAGAAGAGTAAAAGACAGAAGCTCAGTTCAACAAGTGAAGGAAATAAGAAC

Basic information

species Arabidopsis thaliana
transcript AT5G49390.1
intron # 9
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|116464480|gb|EG507072.1|EG507072
EST:     GCTGAGCCCTATAATCCAGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464443|gb|EG507035.1|EG507035
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464458|gb|EG507050.1|EG507050
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464454|gb|EG507046.1|EG507046
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCACGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464465|gb|EG507057.1|EG507057
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464472|gb|EG507064.1|EG507064
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464476|gb|EG507068.1|EG507068
EST:     GCTGAGCCCTATAATCCAGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464489|gb|EG507081.1|EG507081
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464469|gb|EG507061.1|EG507061
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464497|gb|EG507089.1|EG507089
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464448|gb|EG507040.1|EG507040
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTTTGTTTTTCCGAG                         CAAGAGGTTTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464493|gb|EG507085.1|EG507085
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464478|gb|EG507070.1|EG507070
EST:     GCTGAGCCCTATAATCCAGGTGTCACAGCTGCAAGTTTTGTTTTTCCGAG                         CAAGAGGTTTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464485|gb|EG507077.1|EG507077
EST:     GCTGAGCCCTATAATCCAGGTGTCACAGCTGCAAGTTTTGTTTTTCCGAG                         CAAGAGGTTTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464463|gb|EG507055.1|EG507055
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464445|gb|EG507037.1|EG507037
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTTTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464456|gb|EG507048.1|EG507048
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCACGTTTTGTTTTTCCGAG                         CAAGAGGTTTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464467|gb|EG507059.1|EG507059
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTTTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
EST: gi|116464446|gb|EG507038.1|EG507038
EST:     GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAG                         CAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA
genomic: GCTGAGCCCTATAATCCTGGTGTCACAGCTGCAAGTTCTGTTTCTCCGAGgtatttgttt ... aatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagcaacaaatatagttaatagatttgctttctgttttctattaatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGAGAAGAGTAAAAGACAGAAGCTCAGTTCAACAAGTGAAGGAAATAAGAAC
                                         tattaat  putative branch site (score: 2)
      aacaaatatagttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtttctggtttctctcgatagaaattcattagaagcaacaaatatagttaatagatttgctttctgttttctattaatcatatagCAAGAGGTCTGGAGGTTTGGTTGATTATGAGGATGACGAAGATGAGCTAGAGAAGAGTAAAAGACAGAAGCTCAGTTCAACAAGTGAAGGAAATAAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC