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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtacatgatataatatcaaaattacttaaatgtattttcaagttgtggatttaatattcttttatgtaatcttattttgtttatgtctttgcatttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAG

Basic information

species Glycine max
transcript GLYMA01G09290.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G09290.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 8
gtagtacatgatataatatcaaa--attacttaaatgtattttcaagttgtggatttaatattcttttatgtaatcttattttgtttatgtctttgcatttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAG
  | |     |   | |  | |   | |  ||       | |  || |  | | ||    | |  | | |    | | || || | |||  | | |||   |||| |||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || || ||||| ||||| |||
-cattgagaaaagcattgccgacttactggtttttgaagtctggaaatcatagtttgcggagttatatttaaggtttcatattttctatcacgtggcac--agGTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG

upper sequence: GLYMA01G09290.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
gtagtacatgatataatatcaaaattacttaaatgtattttcaagttgtggatttaatattcttttatgtaatcttat--tttgtttatgtctttgcattt-----agGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAG
      |||| |     ||   | ||  ||  | |  |       | ||||  ||||| ||    |  | ||| | ||  ||  | |||||      | ||     |||| |||||||| |||||||||||||||||||| |||||||| || ||||||||||| || || || ||||| || |||
------catgtttgggaatagcagttggttctaagcttggcatcctagtgg--ttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG

upper sequence: GLYMA01G09290.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 8
gtagtacatgatataatatcaaaattacttaaatgtattttcaagttgtggatttaatattcttttatgtaatcttatt--ttgtttatgtctttgca---tttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAG
|||   |   || ||   | | | |    ||   |||| |     |||  |  || |   | | ||  |  ||   | |  ||||||  ||  |||     || ||||||||  |||||||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||| |||||||||
gtaa-gctctatctatagttatactcttatactcgtatgtattctttgaagccttcagcatatgttgagcgatgaaaatgattgtttgagttgttgtggatttaagGTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAG

upper sequence: GLYMA01G09290.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ25923 (Selaginella moellendorffii), 3'ss of exon 7
gtagtacatgatataatatcaaaattacttaaatgtattttcaagttgtggatttaatattcttttatgtaatcttattttgtttatgtctttgcatttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAG
                                               |||  |  ||| |  |  | || |    | | ||   |  | ||||      ||||   |   || || || ||  | || ||||||||||||||||| |||||||| || ||||| || ||||| ||||||
-----------------------------------------------gtgagtc-aatctcttcctttgaag--ctgtgttaactg-gcctttatgcgcagGTGTTTGGAACATTCGCTACATCAGGCTCTGATGGTGCTTTTAACTTCTGGGACAAGGACAGCAAGCAGAGGCTCAAG

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|8283090|gb|BE020651.1|BE020651
EST:     ACAGAGAGAACAATGAGATATATTCAGTCAACTCCTTAAATTTCCATCCG                         GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGG
genomic: ACAGAGAGAACAATGAGATATATTCAGTCAACTCCTTAAATTTCCATCCGgtagtacatg ... ttgcatttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGG
EST: gi|46492909|gb|CN472465.1|CN472465
EST:     ACAGAGAGAACAATGAGATATATTCAGTCAACTCCTTAAATTTCCATCCG                         GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGG
genomic: ACAGAGAGAACAATGAGATATATTCAGTCAACTCCTTAAATTTCCATCCGgtagtacatg ... ttgcatttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGG
EST: gi|193421209|gb|FK389172.1|FK389172
EST:     AAATTTCCATCCG                         GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGG
genomic: AAATTTCCATCCGgtagtacatg ... ttgcatttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggatttaatattcttttatgtaatcttattttgtttatgtctttgcatttagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAG
     atttaat  putative branch site (score: 4)
                                        tgtcttt  putative PPT
     atttaatattctttta  TA-rich tract