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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatttcttattttgagagttgacttattctttaccttcatttcttgatatgtgatagttacagttctctttatttaatatgtcttcacattactttatgctcttttgaagGCTGGCTTGGGACTTCCTGATACAGAAGCTTGGAACATGATCGAGACAATAGCAGAGAAACAAAAGCTTGGATATAAATTACTG

Basic information

species Arabidopsis thaliana
transcript AT1G49040.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA08G04510.1 (Glycine max), 3'ss of exon 20
gtgaatttcttattttgagagttgacttattctttaccttcatttcttgatatgtgatagttacagttctctttatttaatatgtcttcacattactttatgctcttttgaagGCTGGCTTGGGACTTCCTGATACAGAAGCTTGGAACATGATCGAGACAATAGCAGAGAAACAAAAGCTTGGATATAAATTACTG
                           |||| |||    |  |    || |      |  ||  |||    ||   |   | |||  |   | ||||||  ||     ||||||||||  |||||||||||||||  || |||||| |||||||||| ||||| |||||||   | |   | ||||  ||   | | 
--------------------------gtattgtttggtctactcatgtgcttgaatttcattgaagtcaagttgtatctttttgtgcttttaatacttt--gcctgcatgaagGCTGGGCTGGGACTTCCTGATAATGATGCTTGGTACATGATCGAAACAATTGCAGAGAGGAACAGCATCGGATCCAATCAATTT

upper sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 3
gtgaatttcttattttgagagttgacttattctttaccttcat-ttcttgatatgtgatagttacagttctctttatttaatatgtcttcacattactttatgctcttttgaagGCTGGCTTGGGACTTCCTGATACAGAAGCTTGGAACATGATCGAGACAATAGCAGAGAAACAAAAGCTTGGATATAAATTACTG
                       |  || || |     ||||| | |||||  ||   |     ||  |    |  |||    ||| ||   | ||||||  ||     ||||||||||  |||||||||||||||  || |||||| |||||||||| ||||| |||||||   | |   | ||||  ||   | | 
-----------------------gtattgttttggctattcatgtgcttgaattgcattgaagtcaagttgtatctttt----tgtgtttttaatacttt--gcctgcatgaagGCTGGGCTGGGACTTCCTGATAATGATGCTTGGTACATGATCGAAACAATTGCAGAGAGGAATAGCATCGGATCCAAGCAATTT
















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|116437573|gb|EG480165.1|EG480165
EST:     ACTATGCTACTTTGGTCACAGCCAGACTAATCATAGTGGCATCACATATG                         GCTGGCTTGGGACTTCCTGATACAGAAGCTTGGAACATGATCGAGACAATA
genomic: ACTATGCTACTTTGGTCACAGCCAGACTAATCATAGTGGCATCACATATGgtgaatttct ... tcttttgaagGCTGGCTTGGGACTTCCTGATACAGAAGCTTGGAACATGATCGAGACAATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttacagttctctttatttaatatgtcttcacattactttatgctcttttgaagGCTGGCTTGGGACTTCCTGATACAGAAGCTTGGAACATGATCGAGACAATAGCAGAGAAACAAAAGCTTGGATATAAATTACTG
                atttaat  putative branch site (score: 4)
                                     ctttatgctctttt  putative PPT
        ttctctttatttaata  TA-rich tract