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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAGgtcagaccatacaagaatattagaataggaatgtatatattcctttctaataaagaagactcttcttcttttgctttcccttgttacttcatcgtttatgtaagattttttgttttggtttcctttggatcatcatcag

Basic information

species Arabidopsis thaliana
transcript AT3G63080.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G63080.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G329144_T01 (Zea mays), 5'ss of exon 3
CGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAGgtcagaccatacaagaatattagaataggaatgtatatattcctttctaataaagaagactcttcttcttttgctttcccttgttacttcatcgtttatgtaagattttttgttttggtttcctttggatcatcatcag
 || ||||||||| |||||||||| ||||||||||| ||||| | ||| || |  ||  |||||| |  | |      || |     | |   |||   |   |||       |||   || ||| ||      | |    | |   | |   |  ||   |||                                     
TGGGTTCACGGAGACCAATTACACGCAGCTGACGGAGCTTTATCAGAAGTACAGGGACAAAGgtctgttctttgcctgatgtggttcttgatctgttgttgcgcctg------aaatgtgaatct-ctctggaagttggtgcgtagaagtgggtaattggagtagtgca--------------------------------
















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|86027925|gb|DR323678.1|DR323678
EST:     GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG                         GTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCCTG
genomic: GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAGgtcagaccat ... tcatcatcagGTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCCTG
EST: gi|124717957|gb|EH809359.1|EH809359
EST:     ATATAAAGATCAAG                         GTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCCTG
genomic: ATATAAAGATCAAGgtcagaccat ... tcatcatcagGTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCCTG
EST: gi|116467795|gb|EG510387.1|EG510387
EST:     GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG                         GTTTTGTGGTATTGGCGTTTCCTTGCAACCA
genomic: GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAGgtcagaccat ... tcatcatcagGTTTTGTGGTATTGGCGTTTCCTTGCAACCA
EST: gi|19875832|gb|AU236663.1|AU236663
EST:     GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG                         GTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCCTG
genomic: GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAGgtcagaccat ... tcatcatcagGTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCCTG
EST: gi|125201633|gb|EL216587.1|EL216587
EST:     GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAG                         GTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCC
genomic: GTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAGgtcagaccat ... tcatcatcagGTTTTGTGGTATTGGCGTTTCCTTGCAACCAGTTTCTGTCCCAAGAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGATTCACGGAGTCCAATTACACCCAGCTGACGGAACTTTACCGGAAATATAAAGATCAAGgtcagaccatacaagaatattagaataggaatgtatatattcctttctaataaagaagactcttcttcttttgctttcccttgttacttcatcgtttatgtaagattttttgttttggtttcctttggatcatcatcag

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