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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacacttccaaatgacttcactattgttcatataacttaaagtgaagctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGGATTTTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT

Basic information

species Arabidopsis thaliana
transcript AT3G11940.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g01060.1 (Oryza sativa), 3'ss of exon 3
gtaaatacacttccaaatgacttcactattgttcatataac-ttaaagtgaagctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAG-GATTTTCCCTTTGCCCTGTGCGTTA-CAATCTCGTATCAATGAGT
           |  |  |  |||| |  ||| | | || |   ||  |  |     ||| |  || | | || | || |||||||||||||||||||||||||||||||||  | ||||||||||| || |||| || | |   ||| |  |  |||||   | | ||  | |  || ||   
----------gtaaatcttgcttctcatttgatgaaatgaggctactgacacatccatgctctaattctgatatgttacagCTATGCCATCAAGAAGAAGGATGAGATTGAGCGTGTTGCCAAGGCGAACCGTTGAGTGCTGAACCCATCTCAGTGTGCTCGAGCTATTGCCTTGCACTGT--

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g29190.5 (Oryza sativa), 3'ss of exon 2
gtaaatacacttccaaatgacttcactattgttcatataacttaaagtga--agctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAG-GATTTTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT-------------------------------------------
                          | ||||||  || |    | || |    |  ||   ||| ||  | ||| || |||||||||||||||||||||||||||||| ||  | ||||||||||| || |||| || | |  |||| |  |  ||||| | |   ||| |      |  |                                            
------------------------ctttttgttcggatgataccaggttattgacacatctgtgatctaat-tgtgtttcagctatgccatcaagaagaaggatgagatcgagcgtgttgccaagGCCAACCGTTGAGTGGTGATCCCATGTCATTGTGC-TAAAGCTCTTGCGCTGTTTGGCAGGACTATACTTTTTGCTAGTAATTTAAGCCTTTTCAGACCTA

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 3
gta-aatacacttccaa---atgacttcactattgttcatataacttaaagtga--agctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAG-GATTTTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT
||| || ||| |  ||    |   |||   | ||||||  || |    | || |    |  ||   ||| ||  | ||| || |||||||||||||||||||||||||||||| ||  | ||||||||||| || |||| || | |  |||| |  |  ||||| | |   ||| |      |  | 
gtacaacacattgtcatggtacatcttgctttttgttcggatgataccaggttattgacacatctgtgatctaat-tgtgtttcagCTATGCCATCAAGAAGAAGGATGAGATCGAGCGTGTTGCCAAGGCCAACCGTTGAGTGGTGATCCCATGTCATTGTGC-TAAAGCTCTTGCGCTGTTTGGC

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G078985_T01 (Zea mays), 3'ss of exon 3
--gtaaatacact-tccaaatg-acttcactattgttcatataact-taaagtgaagc-taatgattga-actgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAG----GATTTTCCCTTTGCCC-TGTGCGTTACAATCTCGTATCAATGAGT
   || |||  || ||    |  | ||   | || ||    || ||   | |||||   |  | ||| |      |   | |  |||||| ||||||||||||||||| ||||||||  | ||||||||||| || |||| ||    | || |  | | |  |   |||  || ||   ||| ||       
gtatatatatcctgtctggctatatttggttgtttttttcctatctgcgatgtgaattgtgctcattcatggcaattcttgtcacagCTACGCCATCAAGAAGAAGGACGAGATTGAGCGTGTTGCCAAGGCCAACCGTTGAGTGGAGCTTGTATCCTGGTGCACTTGCACTAGAACTACGTTTCTG-----

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G156673_T03 (Zea mays), 3'ss of exon 2
gtaaatacacttccaaatgacttca---ctattgttcatataacttaaagtgaagctaat---gattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAA---GGATTT---TCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT
||| |||   | ||   |  ||||    ||||   | ||    |   | |||||  |  |     | |  |   |   | || ||| || ||||||||||||||||| ||||||||  | ||||||||||| || |||| |   |   ||   |||   ||| || |||| |  || ||  |||        
gtacatatgttgcctgtttgcttcttgtctatctgtgattccgcacgatgtgaaattgttctcattcgtgccaattcttgttacagTTACGCCATCAAGAAGAAGGACGAGATTGAGCGTGTTGCCAAGGCCAACCGTTGAACTGAGCTTGTATCCTGGTGCACTCTGCGCTGGAAACTTTTATGT------

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
---------------------------------------gtaaatacacttccaaatgactt-cactattgttcatataacttaaagtgaagctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGGATTTTCCCTTTGCCCTGTGCGTTACAATCTCG-TATCAATGAGT
                                       |||  |    |||   ||  ||| || | || || ||     ||   ||     ||  ||   ||   |  |   || ||||||||| |||||||| |||||||| ||||| |||||||||||||| || |||| || |  ||      ||  | |  |  |   |   | | |   |  | 
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaa-aaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG-

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S10_385V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------gtaaatacacttccaaatgacttcactat-tgttcatataacttaaagtgaagctaa-tgattgaa--ctgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGG-ATTTTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT
                         |      | || || ||| | ||| | | | || |||    ||| | |       | ||||  ||   ||||   | || |||||| ||||||||||||||||||||||| ||  | || |||||||| ||||||||||  | || |    ||     ||| |          | | ||||   
gtaaaatgcttgagacaaccttgttttgtctgaattacatatggcgtcattctgttttgatacctgttacacttctctggactgataaaaggttgttgcttgttccagCTACGCCATCAAGAAGAAGGATGAGATCGAGCGTGTGGCCAAGGCCAATCGTTAAGCTAGTTGCAAGATGTTTATTGCATCTGGGAACTCTTTAAATGTT-

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ18003 (Selaginella moellendorffii), 3'ss of exon 4
gtaaatacacttccaaatgacttcactattgttcatataacttaaagtgaagctaatgattgaactgttatgtcttgca---gCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGGATTTTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT
        |||||| |    | |   | | | ||||     || ||   ||   |  |      ||||  |   |||||   ||||||| ||||| |||||||| ||||| ||| | ||||||||||| ||||||| |                                             
------gtacttccta----cattgttctagctcatgc--tttgaaagaaactaagagccccttctgtgcttgtttgcatcagCTATGCGATCAAAAAGAAGGACGAGATCGAACGTGTTGCCAAGGCAAATCGTTGA---------------------------------------------

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ17708 (Selaginella moellendorffii), 3'ss of exon 4
gtaaatacacttccaaatgacttcactattgttcatataacttaaagtgaagctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGGATTTTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT
          | ||    | |   |  ||| ||| | |  | | |||     |||| | |     | ||   | || ||||||||| |||||||| ||||||||||||||  | ||||| ||||| ||||||| || |        |       ||        |  | ||||| |    
---------gtacctcgcggccagaa-attcttcctctcgcctcaagct---ctaaagttccttgtttttgatgtttcagCTATGCGATCAAGAAAAAGGATGAGATTGAGCGTGTTGCGAAGGCGAATCGTTGAGAAACACATTCTAATGTAATGAACCTTTTTGGCATATCATTCGAA

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ37091 (Selaginella moellendorffii), 3'ss of exon 4
gtaaatacacttccaaatgacttcactattgttcatataacttaaagtgaagctaatgattgaactgttatgtcttgca---gCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGGATT-TTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT
        |||||| |    | |   | | | ||||     || ||   ||   |  | |    ||||  |   |||||   ||||||| ||||| |||||||| ||||| ||| | ||||||||||| ||||||| | ||   ||   |   ||    |  |     | ||   ||  |    
------gtacttccta----cattgttctagctcatgc--tttgaaagaaactaagagctccttctgtgcttgtttgcatcagCTATGCGATCAAAAAGAAGGACGAGATCGAACGTGTTGCCAAGGCAAATCGTTGAAGAGAATTTTTTCCACCACAGGTTTATTGTTTTCACTTCGCTTGA-

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|301502573|gb|HO208113.1|HO208113
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGA
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGA
EST: gi|86084216|gb|DR379975.1|DR379975
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|86081585|gb|DR377342.1|DR377342
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|124745564|gb|EH836376.1|EH836376
EST:     TGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: TGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|86078785|gb|DR374542.1|DR374542
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|116479315|gb|EG521907.1|EG521907
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|125215746|gb|EL229830.1|EL229830
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAG
EST: gi|124832412|gb|EH916851.1|EH916851
EST:     TGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAG
genomic: TGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAG
EST: gi|164142396|gb|ES083210.1|ES083210
EST:     TCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: TCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|164157551|gb|ES063415.1|ES063415
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGG
EST: gi|125117365|gb|EL166538.1|EL166538
EST:     CAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: CAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|125255709|gb|EL269794.1|EL269794
EST:     CAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTG-AAGAGTTGCCAAGGCTAATCG
genomic: CAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|116465715|gb|EG508307.1|EG508307
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|116397675|gb|EG440267.1|EG440267
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|125040794|gb|EL113063.1|EL113063
EST:     CTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGG
genomic: CTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAA-GAAGAAGGATGAGATTGAAAGAGTTGCCAAGG
EST: gi|116480566|gb|EG523158.1|EG523158
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|125125651|gb|EL171086.1|EL171086
EST:     ACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: ACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
EST: gi|86074460|gb|DR370217.1|DR370217
EST:     GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAG                         CTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG
genomic: GAGTGCCTTGCTGATGAATTGATCAACGCAGCCAAGGGCTCTTCCAACAGgtaaatacac ... tgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgttcatataacttaaagtgaagctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGGATTTTCCCTTTGCCCTGTGCGTTACAATCTCGTATCAATGAGT
                         agctaat  putative branch site (score: 3)
      ttcatataacttaaa  TA-rich tract