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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatttctatctctctttcatttattcatataactatcaagtttcatttcttgctatatatcgatgggattgttggttatgattattgaacttag...

Basic information

species Arabidopsis thaliana
transcript AT3G49010.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 2
TCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttg-taatttctatctctctttcatttattcatataactatcaagtttcatttcttgctatatatcgatgggattgttggttatgattattgaacttag
 || ||| ||||| ||||| | ||| |||| ||||| |||||||| || ||||||||||| |||||| |||| | ||||||  | || |||||  | |||||    | | || |      |      ||    |   |||| | | |  | ||  ||||||||  ||| ||    | || || ||  |  || |   | | 
GCCTACTGCTGGATCTCTCAGGCCTATTGTTCATGGCCAGACTCTGAAATACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgacttattctgaccccattcttgcaaaagcaactgttatgagttatgacttgctatggatc-attcattggtggggtaatacaataggcttgac

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0047g01160.t01 (Vitis vinifera), 5'ss of exon 2
TCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatttct---atctctctttcatttattcatataactatcaagtttcatttcttgctatatatcgatgggattgttggttatgattattgaacttag
 || |||  |||||| || |||||  |||| ||||| || ||| | |||||||||||||| |||||| | || |  |||||| |||| ||||||||||||||  | |  |      ||     |||   |||  |  ||   | | ||  | ||  | |   | | |    |||   || ||  |      |  || |  |  
CCCCACTGTTGGACCACTTCGCCCACTTGTTCATGGACAAACTTTGAAGTACAACATGAAAGTCAGAGCTGGCAGGGGATTCTCTCTGGAAGAGCTCAAGgtgggaacctctctagatgatcatttagcttaagctgatgtttgttaa--tacaagtttaagtgtctga-aatgtttttttttctgggttctcctgtatatga
















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|124921412|gb|EH995032.1|EH995032
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCT
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCT
EST: gi|163969615|gb|ES137857.1|ES137857
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTA
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTA
EST: gi|164209263|gb|ES159864.1|ES159864
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTAC
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTAC
EST: gi|86018575|gb|DR314321.1|DR314321
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCAGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|86074609|gb|DR370366.1|DR370366
EST:     CAACATGAAAGSTCAGAMCCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCAGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: CAACATG-AAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|124978563|gb|EL051722.1|EL051722
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTG
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTG
EST: gi|124967519|gb|EL041549.1|EL041549
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAG
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAG
EST: gi|163990432|gb|ES210592.1|ES210592
EST:     ACAACATGAGGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAG
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAG
EST: gi|86076156|gb|DR371913.1|DR371913
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCAGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|47829477|gb|CK119161.1|CK119161
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|86085358|gb|DR381117.1|DR381117
EST:     TTCACTCTTGAAGAGCTCAAG                         GCTGCAGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: TTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|124798607|gb|EH888286.1|EH888286
EST:     GGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCNCCTACAATTGGTATTG
genomic: GGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTG
EST: gi|164212431|gb|EL989002.1|EL989002
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCC
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCC
EST: gi|47831958|gb|CK121642.1|CK121642
EST:     CTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: CTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|86074296|gb|DR370053.1|DR370053
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCAGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|86018573|gb|DR314319.1|DR314319
EST:     ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCAGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|164154494|gb|ES041477.1|ES041477
EST:     AAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: AAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|164005955|gb|ES013597.1|ES013597
EST:     GAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTAT
genomic: GAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTAT
EST: gi|164021463|gb|ES158323.1|ES158323
EST:     CTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
genomic: CTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTGCTGTTGAC
EST: gi|164215344|gb|ES175729.1|ES175729
EST:     ACAACATGAGGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAG
genomic: ACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAG
EST: gi|124970536|gb|EL044361.1|EL044361
EST:     GGTAAAGGATTCACTCTTGAAGAGCTCAAG                         GCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTG
genomic: GGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatt ... attaatatagGCTGCTGGTATCCCAAAGAAGTTGGCGCCTACAATTGGTATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAGAACCGGTAAAGGATTCACTCTTGAAGAGCTCAAGgtttgtaatttctatctctctttcatttattcatataactatcaagtttcatttcttgctatatatcgatgggattgttggttatgattattgaacttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA