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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaactttgtactcatcatggaaatttaacagttgggcactaaatgagttgcagaattacaacttgtgattgagaatctgtatgtgttttgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTGCTGAGCACAAAACCAGTACAGAGCAGGGGTTCCAGAGGAAACTCGAAGC

Basic information

species Arabidopsis thaliana
transcript AT4G23710.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23710.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G33790.1 (Glycine max), 3'ss of exon 2
tgtaactttgtactcatcatggaaatttaacagttgggcactaaat-gagttgcagaattacaacttgtgattgagaatctgtatgt--gttttgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTGCTGAGCACAAAACCAGTACAGAGCAGGGGTTCCAGAGGAAACTCGAAGC
  || |||| |  |  |  || |    ||  || | |   ||| || || |  |   |||   |      |   || ||| ||||    | | |  | || || |||| || ||||||||||||||||||| ||||| |||||||  ||  |||| ||| | |   |       ||| | | ||| || | |||| |   |  
-ctacctttattgtactattgtactcctattaggtagaatctatatcgaatatctttattggtaa--actaaccagtatcagtattctggatctactgttaagAAAAATTGGCTAGACTGAAGCAAGCCAAAGAAGAGGCTGAAAAGGAAATTGCCGAGTATAGGGCTCAGTTGGAGTACGAGTTTCAAAAGAAAGTGTCACA

upper sequence: AT4G23710.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g01910.t01 (Vitis vinifera), 3'ss of exon 1
tgtaactttgtactcatcatggaaatttaacagttgggcactaaatg-agttgcagaattacaacttgtgattgagaatctgtatgtgttttgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTGCTGAGCACAAAACCAGTACAGAGCAGGGGTTCCAGAGGAAACTCGAAGC
      |   | ||  |  |     | | |||  |       | ||  ||     |  || ||| || || ||   ||||  | ||  ||||    ||||||||||||| ||||||| || |||||||| ||||| |||||||  ||| ||||||   ||  | ||      || |  | |||||||| |||| | |  | 
-aagcataaatgctattgtttttgttcttacaactcaatgtaacatttagaactggttttccaaattttgtttcctaatcactttggttttttgccttcagCAAAAATGGCTAGACTAAAACAAGCCAAAGAAGAGGCTGAAAAGGAGATTGCTGCTTACCGAGCCCAGGTTGAACTTGAGTTCCAGAAGAAATTGGCTGA

upper sequence: AT4G23710.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S24_173V6.1 (Physcomitrella patens), 3'ss of exon 2
tgtaactttgtactcatcatggaaatttaacagttgggcactaaatgagttgcagaatta---caacttgtgattgagaatctgtatgtgttttgattttcagCAAAAAT---GACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTGCTGAGCACAAAAC-CAGTACAGAGCAGGGGTTCCAGAGGAAACT---CGAAGC----------
              | |    |   | |     |||  |  |||    |||   | |||    | | | | |      ||   |||||  |    |  |  | || ||||   |   ||||||| |||||||||||||||||||||   ||| || ||| |  ||| | | |||      || | | ||| ||| ||| ||   |||  |          
--------------ctttgccgctgtct-----ttgatcgataaggttgttttgggattggcgccattcgcggccagaaactagtatgcatgaccacgtctaacataaattctgttcagACTGAGGCAAGCCAAGGAAGAAGCTGAGCGAGAAGTGGCTCAATACAGAGCTCAGCGTGAGGCCGAG-TTCAAGAAGAAGCTGTCCGACACCAGCGGTGAT

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|86074720|gb|DR370477.1|DR370477
EST:     TGAAGCTCAGCAAATTGTCAATGCCGCTAGGACCG                         CAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
genomic: TGAAGCTCAGCAAATTGTCAATGCCGCTAGGACCGgtatttacaa ... tgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
EST: gi|19874789|gb|AU235620.1|AU235620
EST:     GCTTGCTGCTGAACGTGAAGCTCAGCAAATTGTCAATGCCGCTAGGACCG                         CAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
genomic: GCTTGCTGCTGAACGTGAAGCTCAGCAAATTGTCAATGCCGCTAGGACCGgtatttacaa ... tgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
EST: gi|125270200|gb|EL284285.1|EL284285
EST:     TCAATGCCGCTAGGACCG                         CAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
genomic: TCAATGCCGCTAGGACCGgtatttacaa ... tgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
EST: gi|125217518|gb|EL231601.1|EL231601
EST:     AAGCTCAGCAAATTGTCAATGCCGCTAGGACCG                         CAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
genomic: AAGCTCAGCAAATTGTCAATGCCGCTAGGACCGgtatttacaa ... tgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTG
EST: gi|124771808|gb|EH861938.1|EH861938
EST:     AAGCTCAGCAAATTGTCAATGCCGCTAGGACCG                         CAAAAATAGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTT
genomic: AAGCTCAGCAAATTGTCAATGCCGCTAGGACCGgtatttacaa ... tgattttcagCAAAAAT-GACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagttgcagaattacaacttgtgattgagaatctgtatgtgttttgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTGCTGAGCACAAAACCAGTACAGAGCAGGGGTTCCAGAGGAAACTCGAAGC
                                          ttttgat  putative branch site (score: 4)
                                                ttttc  CT-rich tract
                                          ttttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaactttgtactcatcatggaaatttaacagttgggcactaaatgagttgcagaattacaacttgtgattgagaatctgtatgtgttttgattttcagCAAAAATGACTAGACTGAAGCAAGCCAAGGAAGAAGCTGAAACAGAGGTTGCTGAGCACAAAACCAGTACAGAGCAGGGGTTCCAGAGGAAACTCGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - ctcatca
- - - - - - - - - - - - - - - - - - - cactaaa