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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGGATGAATAGCCTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatctcacatttttactagttctcttgtttacattttatattatgcttgaactggttttgtcaaaagcatttttgtatagaattgaaactactag...

Basic information

species Glycine max
transcript GLYMA03G22450.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g33080.1 (Oryza sativa), 5'ss of exon 8
ACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGGATGAATAGCCTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatctcacatttttactagttctcttgtttacattttatattatgcttgaactggttttgtcaaaagcatttttgtatagaattgaaactactag
|  | ||||  || || ||||| ||  |||| ||  ||||||| ||||||||||||| ||| ||||| ||||||||||| |||||||||||  |||||||||   |  || |||||     ||  || |       ||| |||       |   | | | |  | |       |||||  | | |   ||| |       
ATGCTCAAGTTTCGAGGGAAGAGAGGTCATTCCGGTTATGGATTAATAGCCTTGGAATTTCTACATACATCAACAATGTGTTTGAGGATCTTAGAAATGGgtaggt--cttacattaaagttatctccccc-----catcttaatcgtcacccaagccgatgctctatctgatattttgttctggggatgacag------

upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G081380_T01 (Zea mays), 5'ss of exon 8
ACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGGATGAATAGCCTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatctcacatttttactagttctcttgtttacattttatattatgcttgaactggttttgtcaaaagcatttttgtatagaattgaaactactag
|  | ||||  || || ||||||||  |||| || || ||||| || |||||||||| |||||| || ||||||||||| ||||| || ||  |||||||||         ||||    ||| ||   | | || | || | |       |  | ||    ||||||  ||  | ||     | || ||| |        
ATGCTCAAGTTTCCAGGGAAGAAAGGTCATTCCGGCTGTGGATTAACAGCCTTGGAATTTCAACTTACATCAACAATGTGTTTGAAGACCTTAGAAATGGgtagg------acat----acttgtatccatcttaatatgtga------acaagcacattctttgtcttaa-tacttcatccttgagttgtag-------

upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 5'ss of exon 7
ACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGGATGAATAGCCTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatctcacatttttactagt-tctcttgtttacattttatattatgcttgaactggttttgtcaaaagcatttttgtatagaattgaaactactag-------
||||||||  |||||||||||| |||||||||||| | ||||| ||||| |||||||||||||||||||||||||| || ||||| ||| |  ||||||||||| |      || || || |||  | | |||| |  | |   | | || | | |     || | ||| ||  ||||||   |    || ||| ||| |        
ACACCCAAATCTCTAGAGAAGAGAGAGCATTTCGCTTTTGGATAAATAGTCTTGGAAATTCAACATATATCAACAACGTTTTTGAAGATGTGAGAAATGGgtgagtg-----cagttctattagagtatattgtctctactcc-tgtaat-cataagtaatttatatcataa-tattttttcctgacttttaaattacaaataaagaa

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|193478136|gb|FK440681.1|FK440681
EST:     CAACAATGTCTTTGAGGATCTCCGAAATGG                         GTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
genomic: CAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatct ... ttctttacagGTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
EST: gi|193554994|gb|FK511827.1|FK511827
EST:     CTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGG                         GTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
genomic: CTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatct ... ttctttacagGTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
EST: gi|208111440|gb|GD909158.1|GD909158
EST:     CTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGG                         GTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
genomic: CTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatct ... ttctttacagGTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
EST: gi|208332495|gb|GE129908.1|GE129908
EST:     CTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGG                         GTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
genomic: CTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatct ... ttctttacagGTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
EST: gi|193573679|gb|FK531013.1|FK531013
EST:     CAACAATGTCTTTTGTAGGATCTCCGAAATGG                         GTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG
genomic: CAACAATGTC-TTTG-AGGATCTCCGAAATGGgtgaatatct ... ttctttacagGTGGGTTCTTCTTGAGACTCTTGACAAGGTGTCACCAGGGATTGTCAATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACCCAAGACTCTAGAGAAGAAAGAGCATTTCGCCTATGGATGAATAGCCTTGGAAATTCAACATATATCAACAATGTCTTTGAGGATCTCCGAAATGGgtgaatatctcacatttttactagttctcttgtttacattttatattatgcttgaactggttttgtcaaaagcatttttgtatagaattgaaactactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT