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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGGTATCAATCTAACTTCTACAGTCGCTGTCACACACCTTGACCTTGACACC

Basic information

species Arabidopsis thaliana
transcript AT4G39520.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 6
--gtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagt-----ctgactcgatcatggactgttgcta--tgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGGTATCAATCTAACTTCTACAGTCGCTGTCACACACCTTGACCTTGACACC
   |  | |   || || ||| |   | |      | ||| ||      ||  |   |  | ||      | | ||||  |    |  || ||   |||||||| ||||| |||||||||||| | || |||||||| ||||||||||||||  ||||||| || || || ||| |    ||||| || || ||||| || 
caattaaaaaaattgatgtaagattttctg-gttttttattttcttctcttcataacaatttgttcctctttaatcgactaaattcattttctgactgtagGTTAAACAAAGAGCCACCAAATCTGACTTTTAGGAAGAAAGACAAAGGTGGACTCAATCTCACCTCAACTGTCACCACAACACATCTAGATCTTGAGACT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G15180.2 (Glycine max), 3'ss of exon 6
---gtatagattgtt-tatataacaacctttatacactgtatatttgatcgtttctggtagatagtctgactcg----atcatggactgttg-cta--tgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGGTATCAATCTAACTTCTACAGTCGCTGTCACACACCTTGACCTTGACACC
   ||||| ||| |  |||||  ||||   || |   | ||| ||      ||  |   |  | ||   |||      ||| |      ||  |||  |||||||| ||||| |||||||||||| | || |||||||| ||||||||||||||  | ||||| || || || ||| |    ||||| || || || || || 
tatgtatatattttgatatatttcaac---taaattttttattttctcctcttcataacaatttgttccacttaaatcatcttaattcattttctaactgtagGTTAAACAAAGAGCCACCAAATCTGACTTTTAGGAAGAAAGACAAAGGTGGACTTAATCTCACCTCAACTGTCACCACAACACATCTGGATCTCGAGACT
















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|47830368|gb|CK120052.1|CK120052
EST:     ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGG
genomic: ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGG
EST: gi|124755238|gb|EH845368.1|EH845368
EST:     CGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCAAATTTAACATTTAGG-AAAAAGACAAAGGTGG
genomic: CGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGG
EST: gi|164126634|gb|ES046317.1|ES046317
EST:     ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCA
genomic: ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCA
EST: gi|124795030|gb|EH884709.1|EH884709
EST:     ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGG
genomic: ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGGTATCAATCTAACTTCTACAGTCGCTGTCACACACCTTGACCTTGACACC
                       gtctgac  putative branch site (score: 3)