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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcagatagaatttggataatatttacaagattagcctctgcggtggttggatttgtttgttgttgcatcctctgtgcttaatgttttgtgtttgcgttag

Basic information

species Glycine max
transcript GLYMA11G12260.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g50616.1 (Oryza sativa), 5'ss of exon 3
GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcagatagaatttggataatatttacaagattagcctctgcggtggttggatttgtttgttgttgcatcctctgtgcttaatgttttgtgtttgcgttag
||||||||||||| | || ||||||||||| | |||||| ||||||||| | || |||||   ||||||||||||||| ||  ||||||  ||    ||||||||       |||   ||||  ||||   | ||     | |  |  ||| | |  ||| ||  | ||  | | ||    | || |  | | |    |   ||||
GTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACAT---AGAGgtaaa-----gcagagactggaccatatgctccagt---acgtaggtagtgatagtctttcttcat-gtaac-ttctggaagtttgacatctggatcat---ttag

upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 5'ss of exon 4
GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatg---cagatagaatttggataatatttacaagattagcctctgcggtggttggatttgtttgttgttgcatc-ctctgtgcttaatgttttgtgtttgcgttag
 || || ||||| ||||  ||||| ||||| | ||||||||| |||||| |||| |||||  |||||||||||||||  ||||| || || ||| | ||||| | ||     | | |    |  | || | ||    ||||    |  ||  |   |     ||  |||   | |||  ||||||                         
ATTTCTAAAAGCAAGGAGATTTGACATTGAGAAAGCAAAGCAAATGTGGACTGACATGCTTAAATGGAGGAAGGAGTACGGTACAGATACAATTGTTGAGgttagtgttcttgcttgtgcctataaaacaattt--ggattttgtttggctataaataa---tgcctgtaactacatttctctgtag-----------------------

upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G157043_T01 (Zea mays), 5'ss of exon 3
GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcagatagaatttggataatatttacaagattagcctctgcggtggttg-gatttgtttgttgttgcatcctctgtgcttaatgttttgtgtt-tgcgttag
|||||||||||| || || ||| ||||||| | |||||| ||||||||| | || |||||   |||||||||||| |||||| |||||| |||    |||||||| ||  ||    ||||  ||||||    ||   ||  | |   | |   ||   | || |  ||  |      |   |  | || || |  | |  | | ||||
GTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATAT---AGAGgtaaa-gctaat----tttg--taatataccaaaacatataccccatgatatatgtagtgtgatcatttcttttcgtttaattttaaaagtctaatctggtcctttag

upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcagatagaatttggataata-tttacaagattagcctctgcggtggttggatttgtttgttgttgcatcctctgtgcttaatgttttgtgtttgcgttag
|||| ||||||||||||| |||||| |||| | ||| || || ||||||||||||||| | ||||||||||| |||||||||||||||||||||||  |||||  |||   || |     |||| || |||| |  |||    ||||   | ||    |||  ||  | | |                                   
GTTCTTGAAAGCGAGGAAATTTGATGTTGAGAAAGCTAAACAAATGTGGGCTGATATGATTCAATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAGgta--tgctattaaatagaagatagtagtttaaaccattgttgtctgtttttgtaacgttttatttctctcgttag-------------------------------

upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 4
GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcagatagaatttggataatatttacaagattagcctctgcggtggttggatttgtttgttgttgcatcctctgtgcttaatgttttgtgtttgcgttag-----
|||| ||||||| ||||||||||||||||| | ||||||||| |||||| |||||||| | || ||||||||||| |||||| ||||||| ||| ||||||||        | ||  |  ||| || ||  |   ||| |    || | |  ||  |  |  || | |   |   || || | ||||| | || | | ||| || |     
GTTCTTGAAAGCAAGGAAGTTTGATATTGAGAAAGCAAAGCACATGTGGACTGATATGATTCAGTGGAGGAAGGATTTTGGTGCTGACACAATTTTGGAGgta--------tcgatatctgatgat-ttgcctgaatttggtgatg-gattattcaaaatacttttggcatctggctttgag-ttaatatattttctatgcttttgtaaag

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|193601711|gb|FK552192.1|FK552192
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG                         GATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
genomic: CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcag ... tttgcgttagGATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
EST: gi|193634461|gb|FK580232.1|FK580232
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG                         GATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
genomic: CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcag ... tttgcgttagGATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
EST: gi|208265768|gb|GE062241.1|GE062241
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG                         GATTTTGAGTTCAAAGAAATAGATGAGGTGGTGAAT
genomic: CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcag ... tttgcgttagGATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAAT
EST: gi|208288228|gb|GE083107.1|GE083107
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG                         GATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATT
genomic: CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcag ... tttgcgttagGATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATT
EST: gi|193633223|gb|FK578819.1|FK578819
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG                         GATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
genomic: CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcag ... tttgcgttagGATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
EST: gi|193369813|gb|FK337173.1|FK337173
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG                         GATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
genomic: CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcag ... tttgcgttagGATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
EST: gi|208062412|gb|GD860504.1|GD860504
EST:     CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG                         GATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC
genomic: CTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcag ... tttgcgttagGATTTTGAGTTCAAAGAAATAGATGAAGTGGTGAATTATTATCCACATGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAGgtaaatgcagatagaatttggataatatttacaagattagcctctgcggtggttggatttgtttgttgttgcatcctctgtgcttaatgttttgtgtttgcgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG