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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcattataaacaattggtctatggttcagttgtttaatgaattgttggatttggtactgatttcgtacttgttctgttttcgtttgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGAGACTACTTGCCTATTGTACGTGAGAAGCCTACCATGGAACTCGTCAAGC

Basic information

species Arabidopsis thaliana
transcript AT3G49010.1
intron # 4
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|86076156|gb|DR371913.1|DR371913
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|125031776|gb|EL104045.1|EL104045
EST:     TACAAGACCAAGTTAGTCATTTTCCCGCGTCGTTGCCCGACAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: TACAAGACCAAGTTAGTCATTTTCCCGCGTCG-TGCCCG-CAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|164182477|gb|ES018246.1|ES018246
EST:     CGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|86085358|gb|DR381117.1|DR381117
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|116471273|gb|EG513865.1|EG513865
EST:     CCTACAAGACCGAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|47829477|gb|CK119161.1|CK119161
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|124993436|gb|EL065705.1|EL065705
EST:     CCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|86018573|gb|DR314319.1|DR314319
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACC-AAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|164222836|gb|ES042185.1|ES042185
EST:     CCTACAAGACCAAGTTAGTCATTT-CCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGG
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGG
EST: gi|125028276|gb|EL100545.1|EL100545
EST:     CCTACAAGACCAAGTTAGTCATCTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTT
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTT
EST: gi|164057454|gb|ES153098.1|ES153098
EST:     GTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: GTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|86074296|gb|DR370053.1|DR370053
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|164014387|gb|ES056673.1|ES056673
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGG
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGG
EST: gi|164034410|gb|ES197174.1|ES197174
EST:     TACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTAACAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCC
genomic: TACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGT--CAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCC
EST: gi|164187663|gb|ES195467.1|ES195467
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCC
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCC
EST: gi|124959490|gb|EL034194.1|EL034194
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCCTACCCAAGTTCAA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGC-TACCCAAGTTCAA
EST: gi|163981564|gb|ES029114.1|ES029114
EST:     CCTACAAGACCAAGTTAGTCATTT-CCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTT
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTT
EST: gi|86018575|gb|DR314321.1|DR314321
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|164105591|gb|ES012898.1|ES012898
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACC
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACC
EST: gi|164197245|gb|ES094321.1|ES094321
EST:     TTTTCCCGCGTCGTGCCCGCAAGATCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: TTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|164201644|gb|ES171439.1|ES171439
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGAACTCTACACCAGAAGAGTTGGCTAATGC
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGA-CTCTACACCAGAAGAGTTGGCTAATGC
EST: gi|164218854|gb|ES190080.1|ES190080
EST:     CCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|163968033|gb|ES166146.1|ES166146
EST:     CTACAAGACCAAGTTAGTCTATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTC
genomic: CTACAAGACCAAGTTAGTC-ATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTC
EST: gi|86074609|gb|DR370366.1|DR370366
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|163969160|gb|ES014874.1|ES014874
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAG
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAG
EST: gi|125000894|gb|EL073163.1|EL073163
EST:     CCTACAAGACTAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAA
EST: gi|47831958|gb|CK121642.1|CK121642
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|164152426|gb|ES008790.1|ES008790
EST:     GTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATG
genomic: GTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATG
EST: gi|163971858|gb|ES148330.1|ES148330
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCC
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCC
EST: gi|124824472|gb|EH909338.1|EH909338
EST:     GTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGTTAATGCTACCCAAGTTCAAGGA
genomic: GTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGA
EST: gi|125150914|gb|EL183317.1|EL183317
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAG
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAG
EST: gi|125040736|gb|EL113005.1|EL113005
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTT
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTT
EST: gi|124722157|gb|EH813559.1|EH813559
EST:     CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAG                         GCTGGTGACTCTACACCAGAAGAGTTGGCTAA
genomic: CCTACAAGACCAAGTTAGTCATTTTCCCGCGTCGTGCCCGCAAGGTCAAGgtaatcatta ... tgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgttggatttggtactgatttcgtacttgttctgttttcgtttgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGAGACTACTTGCCTATTGTACGTGAGAAGCCTACCATGGAACTCGTCAAGC
               tactgat  putative branch site (score: 2)
                                ttctgttttcgttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcattataaacaattggtctatggttcagttgtttaatgaattgttggatttggtactgatttcgtacttgttctgttttcgtttgtgtgttagGCTGGTGACTCTACACCAGAAGAGTTGGCTAATGCTACCCAAGTTCAAGGAGACTACTTGCCTATTGTACGTGAGAAGCCTACCATGGAACTCGTCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA