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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacagatgttaatgaagaaaattccaaagaaataactaaatacagaagcaaattcaactcttaacctttgttgtatccttttctccatttttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 1
cacagatgttaatgaagaaaattccaaagaaataactaaatacagaagcaaattcaactcttaacctttgttgtatccttt----tctccatttttgtgtgt--agGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG
   ||     |     |   |||| |        | ||  | ||| |  |||| | ||   ||   |||||| | |    |    | |   ||| ||||  |  ||||||| ||||||| |||||||||||| ||||||||| | ||||| ||| ||||  |||| || |||||||||
---aggaaccagccttgtctattctatgtgttatattatgtgcagta-taaatgccaca--tattttttgttatcttgactaaaatgtttgtttatgtgctttcagGGATATGCAGCTAGGGAGTTTGCCAAGCAAGGGGTTAAGCCAGGGGAACTGGCAATTATTTCCAAAGAGGCG
















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|86038366|gb|DR334121.1|DR334121
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|124929182|gb|EL006753.1|EL006753
EST:     CGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: CGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038353|gb|DR334108.1|DR334108
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038384|gb|DR334139.1|DR334139
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038379|gb|DR334134.1|DR334134
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGATTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038373|gb|DR334128.1|DR334128
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038364|gb|DR334119.1|DR334119
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038359|gb|DR334114.1|DR334114
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038370|gb|DR334125.1|DR334125
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038368|gb|DR334123.1|DR334123
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|124764747|gb|EH854877.1|EH854877
EST:     CGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: CGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038377|gb|DR334132.1|DR334132
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|152033821|gb|BP816817.2|BP816817
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038378|gb|DR334133.1|DR334133
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTNAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038374|gb|DR334129.1|DR334129
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038367|gb|DR334122.1|DR334122
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038358|gb|DR334113.1|DR334113
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038363|gb|DR334118.1|DR334118
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAASCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038380|gb|DR334135.1|DR334135
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038376|gb|DR334131.1|DR334131
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTN-AACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038355|gb|DR334110.1|DR334110
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038356|gb|DR334111.1|DR334111
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038354|gb|DR334109.1|DR334109
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTKCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038381|gb|DR334136.1|DR334136
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGATTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038383|gb|DR334138.1|DR334138
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGATTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038357|gb|DR334112.1|DR334112
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038369|gb|DR334124.1|DR334124
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038361|gb|DR334116.1|DR334116
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGATTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038362|gb|DR334117.1|DR334117
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038382|gb|DR334137.1|DR334137
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|301501396|gb|HO206936.1|HO206936
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
EST: gi|86038375|gb|DR334130.1|DR334130
EST:     TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCC                         GGATACGCAGCTAAGGATTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG
genomic: TGGCGGAGAAGAGCTTTAAGTACATCATCCTCGGCGGCGGCGTCTCTGCCgtgagtatct ... ttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcaaattcaactcttaacctttgttgtatccttttctccatttttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG
             tcttaac  putative branch site (score: 2)
                   cctttgttgtatcctt  CT-rich tract
                                         atttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacagatgttaatgaagaaaattccaaagaaataactaaatacagaagcaaattcaactcttaacctttgttgtatccttttctccatttttgtgtgtagGGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - aagaaaa
- - - - - - - - - - - - caaagaa
- - - - - - - - - - - - - - - - -aactaaa
- - - - - - - - - - - - - - - - - - - - - - -aagcaaa