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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G12250.5
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
gtgatagattcatctctgtggatcaactagcat-ctgtgtatattacgcatatgcataatctgttttgt-ttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
|||| |  || |  || ||   ||   | | || |  |||   |||  | | ||  | ||   |||  | ||   ||| |   ||  | ||||||  ||||  ||||||||||||||||||||||||||||||||||  |  ||||||| |||
gtgacat-tttagttccgtt--tcttttcgtatacaatgtcacttaatcttgtg--tgattaatttcatattgtattttggcatg--caatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
||| ||  ||     || |   |     ||   ||   |||  |      ||| ||  | | ||  |     | || ||| |  ||  |||    | ||  |||||||||||||||||||||| |||||||||||  |  |||| || |||
gtgttaatttatctcctatttcttgtgcagtg-ctacttatcctttcttaatg-atggtat-ttaggaagtatgtttgttat--tctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

upper sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
gtgatagattcatctc-tgtggatcaactagcatctgtgtatattacgcatatgca-taatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
||  ||  ||  |||| | |   ||      | |  |||| | ||||   |   || | ||    | |   |  |     |  |  ||  |||    | ||  ||||||| ||||||||||||||||||||||||||| |  ||||||| |||
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG

upper sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
|| |||   |  |  || |   ||||   |    | | || |    | || ||| |  | |   |||  |  ||    |||     | |||||  | ||  ||||||| ||||||||||||||||||||||||||  |  ||||||| |||
gtaatatcgtggttcctttttctcaa---gttcttattta-accttgtat-tgcttgttattaattgcatttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 4
gtgatagattcatctc-tgtggatcaactagcatct-gtgtatattacgcatatgca-taatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
    |   || ||||| | ||  |    ||   | | |||| | ||||   |   || | ||    | |   |  |     |  |  ||  |||    | ||  ||||||| |||||||||||||||||||| |||||  |  ||||||| |||
---gtttttttatctcatatgtcttctgtactctttagtgtttgttaccatttcacaatgatggaatctagataatgcatttgatattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGGAAAAGTCGGCTGAGGAAAAAG

upper sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
-------------gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
                 ||  || |  |  ||    |   ||  ||||     | | |    |||   | |  || ||  |    ||||  || |       |||| || || ||||||||||| |||||||||||||||||||||||  | ||||| ||||| 
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattat----tgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
gtgatagattcatctctgtggatcaactagcatctgtgt-atattacgcatatgca-taatctgttttgtttcctt-ttcgttt-tgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
         |||| |   |  | | | | || | | | | || | |     ||||| |||  | |  || |   || || |||| |  | || |||| |||||||||||||||||||||||||| || ||| |||||||| ||||||| ||||| 
--------gtcatatagatcaaactaattgcgtgtatatcatctcaactgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA

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|125253210|gb|EL267295.1|EL267295
EST:     CTGCTGCCTCTGATTCCAGTGATCGATCAAAGGATAAGTTGGATCAAAAG                         ACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCA
genomic: CTGCTGCCTCTGATTCCAGTGATCGATCAAAGGATAAGTTGGATCAAAAGgtgatagatt ... tgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCA
EST: gi|124915313|gb|EH989187.1|EH989187
EST:     CTGCCTCTGATTCCAGTGATCGATCAAAGGATAAGTTGGATCAAAAG                         ACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCA
genomic: CTGCCTCTGATTCCAGTGATCGATCAAAGGATAAGTTGGATCAAAAGgtgatagatt ... tgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCA
EST: gi|116415731|gb|EG458323.1|EG458323
EST:     CTGCTGCCTCTGATTCCAGTGATCGATCAAAGGATAAGTTGGATCAAAAG                         ACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTG
genomic: CTGCTGCCTCTGATTCCAGTGATCGATCAAAGGATAAGTTGGATCAAAAGgtgatagatt ... tgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
                                          ttttgat  putative branch site (score: 4)
                      tctgttttgtttcctt  CT-rich tract
                          ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG