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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtcagatcctccgatcatcttctctctagttaattattatttcttgattctaaattttttgttaacaaacaatttggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G63080.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G63080.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G329144_T02 (Zea mays), 3'ss of exon 2
---------gtccgtcagatcctccgatcatcttctctctagttaattattatttcttg--attctaaattttttgttaacaaacaatttggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG--------------------------------------
          |    | ||   |  ||  |  || |   | ||    |  |  |||  |  || || |     || || |    |    ||  |  ||| || ||||||||| |||||||||| ||||||||||| ||||| | ||| || |  ||  |||                                      
gtacgctatctttccctgacagttggaagaatttgttcttggtattctcgtggttcgggagatgctgagacagtt-ttgatgttctcgatgccgt-cagTGGGTTCACGGAGACCAATTACACGCAGCTGACGGAGCTTTATCAGAAGTACAGGGACAAAGGTCTGTTCTTTGCCTGATGTGGTTCTTGATCTGTTGTT

upper sequence: AT3G63080.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G329144_T01 (Zea mays), 3'ss of exon 2
---------gtccgtcagatcctccgatcatcttctctctagttaattattatttcttg--attctaaattttttgttaacaaacaatttggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG
          |    | ||   |  ||  |  || |   | ||    |  |  |||  |  || || |     || || |    |    ||  |  ||| || ||||||||| |||||||||| ||||||||||| ||||| | ||| || |  ||  |||
gtacgctatctttccctgacagttggaagaatttgttcttggtattctcgtggttcgggagatgctgagacagtt-ttgatgttctcgatgccgt-cagTGGGTTCACGGAGACCAATTACACGCAGCTGACGGAGCTTTATCAGAAGTACAGGGACAAAG
















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|124719433|gb|EH810835.1|EH810835
EST:     GCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGACTTCTAAATG                         CGGATTCACGGAGTCCAATTAC
genomic: GCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCG-CTTCTAAATGgtccgtcaga ... tggggaacagCGGATTCACGGAGTCCAATTAC
EST: gi|125035728|gb|EL107997.1|EL107997
EST:     AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATG                         CGGATTCACGGAGTCCAATTACACCC
genomic: AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATGgtccgtcaga ... tggggaacagCGGATTCACGGAGTCCAATTACACCC
EST: gi|86027925|gb|DR323678.1|DR323678
EST:     AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATG                         CGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATA
genomic: AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATGgtccgtcaga ... tggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATA
EST: gi|116467795|gb|EG510387.1|EG510387
EST:     AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATG                         CGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATA
genomic: AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATGgtccgtcaga ... tggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATA
EST: gi|19875832|gb|AU236663.1|AU236663
EST:     AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATG                         CGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATA
genomic: AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATGgtccgtcaga ... tggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATA
EST: gi|116473167|gb|EG515759.1|EG515759
EST:     AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATG                         CGGATTCACGGAGTCCA
genomic: AGCGTGTATCAAGGGAAAGTGCTGCTCGTCGTCAACGTCGCTTCTAAATGgtccgtcaga ... tggggaacagCGGATTCACGGAGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattattatttcttgattctaaattttttgttaacaaacaatttggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG
                              tgttaac  putative branch site (score: 2)
     tattatttcttgattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtcagatcctccgatcatcttctctctagttaattattatttcttgattctaaattttttgttaacaaacaatttggggaacagCGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA