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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG

Basic information

species Arabidopsis thaliana
transcript AT2G28760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
--acattcattacccgtgg-tgatgcaacaactatactaacacaaatca-ctatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
  | |  ||       ||  |||   ||   ||       || || | |  | |  |  |||   || |  |     |||| ||  ||  | ||||  |||  ||| || ||||| |||||| | || ||||||||||||||||||||||| || || ||||||| ||||||| |||| ||||| |||||              
ttataaacagggattttgtctgaaagaatcccttagtctgcataacttaatttttcttgatgccttgtttaaccaacatttctttcat--tcttgaccata--gTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG-------------

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 2
acattcattacccgtggtgatg-caacaactatactaacacaaatcactatgatccatgt-agtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
||| |  |  |  ||   |||| |  |   || |    ||    |  |  |      ||| | |  | |   ||  | ||||   |   | |   |  |||||| |||||||| ||  |||| || |||||||||||||| ||||| || || || ||||| ||||||||| |||| ||||| |||||              
acaatgct--cttgtcaggatgtcttcctttacatggtcattttttccctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG-------------

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 3
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattg--atttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
  ||| | ||    |  ||  | | |||||||  |  || ||  | || |      | | |  |      ||   | |  ||   | ||| |  | | |||||| || ||||| |||||||| || |||||||||||||||||||| || ||  | ||||| | ||||||| |||| ||||| |||||              
caattgaatattgcttttgcagaagcaactattttg-cataagcctctttttcttgtattgatgccttgtttaccagtatttctttcattcttgata-acagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG-------------

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 2
-------acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
       |      ||  | |     || |   |       ||||| || |   | ||    |||   || |  |     |||| ||  ||  | ||||  |||  ||| || ||||| || ||| | || ||||||||||||||||||||||| || || || |||| ||||||| |||| ||||| |||||              
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctgg---atgccttgtttaaccaacatttctttcat--tcttgaccata--gTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG-------------

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaa-attgatt--tgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
    | | |     |  ||  | | |||||||  |  ||  |  | || |  ||  |||  || |      || |    | ||   | ||| |  | | | |||| || ||||| |||||||| || |||||||||||||||||||| || ||  | ||||| | ||||||| |||| ||||| |||||              
tttgtgaatgtggcttttgcagaagcaactattttg-catgagcctcttttttct-tgtcttgatgccttgtttaccagtattctttcattcttgata-atagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG-------------

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 2
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
  || |  |   |  | ||    |      ||  | |      || || |  |      | |  | |   ||    ||||   |   | |   |  | |||| |||||||| ||  |||| || |||||||||||||| ||||| || || || ||||| ||||||||| |||| ||||| |||||              
caatgctcttgtcaggatgtcttactttacatgatcatttttttccctttccttacgtgaattcttggttttacaatgttcctttcatctctgacaaaagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG-------------

upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
-acattcattac--ccgtggtgatgcaacaactatactaacacaa-atcactatgatccatg--tagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
  || |||| ||   | ||   |  || ||  |  ||||   ||  |    ||| |||  |   || |     | | | |||  ||  |   | ||||     ||||| |||||||| || ||||| || ||||||||||||||||||||||||||| | || || ||  ||||| |||| |||||||||||              
tccaatcatcacattcatgccaacacatca-ttgcactagatcattacttttattatctttaactaattcct-acagtaattcctttcac--tcttgatg--gcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG-------------

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|86061220|gb|DR356977.1|DR356977
EST:     CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAG                         TCGAATATGAGGATCTTGGTGACCGGA-GAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAGgttagttctg ... gaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|86061221|gb|DR356978.1|DR356978
EST:     CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAG                         TCGAATATGAGGATCTTGGTGACCGGA-GAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAGgttagttctg ... gaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|152038570|gb|AV831033.2|AV831033
EST:     CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAG                         TCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAGgttagttctg ... gaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACAT
EST: gi|86061222|gb|DR356979.1|DR356979
EST:     CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAG                         TCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACAT
genomic: CAAAGCCACCACCTATGCCGTCTCCTCTGCGTAATTCCAAGTTTTTTCAGgttagttctg ... gaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
                       aattgat  putative branch site (score: 4)
                                    aatgattttgaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA