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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacagatcatttacttgagttttatattgcataatgggttctcagacagatataaacattttggttttggtttgtttagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG

Basic information

species Arabidopsis thaliana
transcript AT1G02305.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02305.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G108849_T04 (Zea mays), 3'ss of exon 5
-----gtaacagatcatttactt----gagttttatattgcataatgggttctcagacagatata-aacattttggt---------tttggtttgtt-----tagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG
       | |||||||  ||  |     ||| |   ||    || | |   || | | ||  ||  |||||  | ||         | | || || |      ||||||||||||| ||||| ||||| ||||||||||| || |  ||    ||| | || |||||  |    ||||||
cttcatgagcagatcaagtaagttcaacagtctagcatatattattagtgcctaaaagagcgatgcaacatgcttgtagtataatgtcttgtctgatgacAACAGGGTCACTGTGGCTCTTGTTGGGCTTTTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG

upper sequence: AT1G02305.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 5
gtaa----cagatcattt---acttgagttttatattgcat---aatgggttctcagacagatataaac--attttggttttggtttgtttagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG
||||    || ||  | |   |||    | ||  | | |||   | |      ||| | || | | | |  ||  | ||  || |   || ||||||||||||||||||| ||||| |||||||||||||||||| |||| ||  | || |||||  | | | |  | 
gtaatcctcatattttctcacactaacatctttaaatacattcaattcaaggttcaaagagttttcagctgatccttgtgctgatg-attcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTA

upper sequence: AT1G02305.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
--------------gtaacagatcatttacttgagttttatattgcat-aatgggttctcagacagatataaacattttggttttggtttgtttagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG
               |  || |       ||| |  |  ||      | ||  |  | ||   | |||     |||  | ||  || |   || ||||||||||||||||||| ||||| |||||||||||||||||| |||| ||  | || |||||  | | | |  | 
gtgatcctcatattttctcacactgacatctttaaatacattcaatgttaaaagagtttctagctgatcctt-catccttgtgctgatg-attcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT

upper sequence: AT1G02305.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaacagatcattta-cttgagttttatat---tgcataatgggttctcagaca----gatataaacattt--tggttttggtttgtt----tagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG
          |  ||  | ||||| | |      |||||   || || | |  |||||||| |    | | ||   ||||  |  ||||  ||| ||     ||||||| ||||| ||||| ||||| ||||||||||||||||| ||||| ||  | || || ||| | | |  ||||
gtaacttggtttgcattttatttagcgttgtccctatataaatgaatgaggaattctcagaaatttgggtttatttatttatttatttttattttttaaatcagGGTCATTGTGGCTCTTGTTGGGCTTTTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG

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|164076259|gb|ES113612.1|ES113612
EST:     AAGGANCTTAGATCAG
genomic: AAGGATCTTAGATCAG
EST: gi|86037996|gb|DR333751.1|DR333751
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTCTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038014|gb|DR333769.1|DR333769
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|124920080|gb|EH993818.1|EH993818
EST:     GGAAGGATCTTAGATCAG
genomic: GGAAGGATCTTAGATCAG
EST: gi|86037980|gb|DR333735.1|DR333735
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038002|gb|DR333757.1|DR333757
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037992|gb|DR333747.1|DR333747
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038004|gb|DR333759.1|DR333759
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|116429058|gb|EG471650.1|EG471650
EST:     TTTGATTACTGGAACTCGTCGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038015|gb|DR333770.1|DR333770
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037994|gb|DR333749.1|DR333749
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037990|gb|DR333745.1|DR333745
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037989|gb|DR333744.1|DR333744
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|164086098|gb|ES205657.1|ES205657
EST:     TTGGAAGGATCTTAGATCAG
genomic: TTGGAAGGATCTTAGATCAG
EST: gi|86037997|gb|DR333752.1|DR333752
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037987|gb|DR333742.1|DR333742
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTCTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037986|gb|DR333741.1|DR333741
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037984|gb|DR333739.1|DR333739
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037998|gb|DR333753.1|DR333753
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038000|gb|DR333755.1|DR333755
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038013|gb|DR333768.1|DR333768
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86037991|gb|DR333746.1|DR333746
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038017|gb|DR333772.1|DR333772
EST:     TAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|86038010|gb|DR333765.1|DR333765
EST:     TTTGATTACTGGAACTCGTTGAGGGATTGAGNNNNNNNTAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
genomic: TTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTC
EST: gi|163997698|gb|ES197872.1|ES197872
EST:     TTGGAAGGATCTTAGATCAG
genomic: TTGGAAGGATCTTAGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcataatgggttctcagacagatataaacattttggttttggtttgtttagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG
                                              tttgttt  CT-rich tract
                       agatataaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacagatcatttacttgagttttatattgcataatgggttctcagacagatataaacattttggttttggtttgtttagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT