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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccctggtgtttctttcagaacctctaatattattttaccatttttctgtttacttaataatttgttgtggtattttttgagcttcaggcattt...

Basic information

species Glycine max
transcript GLYMA10G01820.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcac------------cctggtgtttctttcagaacctct-aatattattttaccatttt--tctgtttacttaataatttgttgtggtattttttgagcttcaggcattt--------------------------------------------------------------------------------
|||||| |||||||| |||||||| || || |||||||||||||||   || |||||||||||||||||||| || ||||  |||||  |  |            |||| |  || |||  | |   ||  | | ||||||  ||| |   ||    |||| |  |  | ||      ||  || || | |     |||                                                                                 
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcag-aggtggtcagaaaatggttagaacat-gcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag

upper sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccctggtgtttc--tttcagaacctctaatattattttaccatttttctgtttacttaataatttgttgt-ggtattttttgagcttcaggcattt
|||||| |||||||| |||||||| || ||||| ||||| || |||   || ||||||||||||||||| ||  ||||||  ||||| |    | || | |||   | |  | |  | |||| | |        || |    | |  |   |  ||   ||   ||| || |  | | |  | |||  
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAGgtaaatctcatgttttttaggtgtttggaaatttaatgtcaaggccgttttgtgtcatatcttcgctgtttgcatgccagtagttctctatcgtttg-cat--

upper sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcag---caccctggtgtttctttcagaacctctaatattattttaccatttttc--tgtttactt--aataatttgttgtggtattttt-tgagcttcaggcattt----------------------------------------------------------
|||||| ||||||||||||||||| || || |||||||| |||||   |||||||||||| || ||||||||  | || |  |||||      |||| || |   |||  |        |  |  ||||  | || |||||    ||||| |   | |||||  | ||||||        | |      || |                                                          
GTGTGGCCACTGCAAAAAGCTTGCCCCCGAGTATGAAAAACTTGGCGCCAGCTTCAAGAAGGCTAAATCTGTACTGATAGCAAAGgtacatctcaccttgtttagtctccccaggggaatgttggtattgcaacagttttcatcatttacatcccacaattttctatggtatcgaaacttgttctgaatatctaattacatttctttgctgcaatgaattaactgttttcctttttgtatctactacctag

upper sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccctggtgtttctttcagaacctctaatattattttaccatttttctgtttacttaataatttgttgtggtattttttgagcttcaggcattt
|||||| |||||||| || ||||||||||| ||||||||||| ||    ||||||||||| || || ||||| || ||||  ||||| ||     |  | ||||  |    | ||| ||| |    |||  |  |   ||  |  |  ||  |||    | || | || ||    | | |     
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatttcggtattcagctccaatgt----ttaaaagatagatgaatgatagattgtttcaacttgtgtattgtgg---tgaag-----

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|207720341|gb|GD702168.1|GD702168
EST:     TAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: TAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|7685788|gb|AW756436.1|AW756436
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|16347802|gb|BI973397.1|BI973397
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|193718783|gb|FK655217.1|FK655217
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAG
EST: gi|209718584|gb|BW674723.1|BW674723
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|213613771|gb|DB961268.1|DB961268
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|208290284|gb|GE082292.1|GE082292
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|208296783|gb|GE095693.1|GE095693
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|208279072|gb|GE077535.1|GE077535
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|193426412|gb|FK386583.1|FK386583
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGAACTGTGATGA
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGA-CTGTGATGA
EST: gi|209701913|gb|BW664567.1|BW664567
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|193316002|gb|FK280724.1|FK280724
EST:     AAATACTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAT-CTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|213596787|gb|DB964078.1|DB964078
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|208169370|gb|GD969627.1|GD969627
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGT
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGT
EST: gi|298194838|gb|HO043310.1|HO043310
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|298198107|gb|HO039646.1|HO039646
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|208064551|gb|GD862495.1|GD862495
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATA
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATA
EST: gi|298167695|gb|HO012958.1|HO012958
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|193304585|gb|FK272630.1|FK272630
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGAT
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGAT
EST: gi|208191744|gb|GD991062.1|GD991062
EST:     GTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: GTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|193717561|gb|FK650341.1|FK650341
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|22540736|gb|BU090579.1|BU090579
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|193499450|gb|FK460363.1|FK460363
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|298163482|gb|HO012215.1|HO012215
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|208196078|gb|GD991713.1|GD991713
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGT
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGT
EST: gi|208060889|gb|GD858799.1|GD858799
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|151396040|gb|EV265917.1|EV265917
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|213587217|gb|DB965921.1|DB965921
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|151397387|gb|EV267260.1|EV267260
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAGGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|151406560|gb|EV276375.1|EV276375
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|298195370|gb|HO039201.1|HO039201
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
EST: gi|209711953|gb|BW679032.1|BW679032
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccc ... tgtaatgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccctggtgtttctttcagaacctctaatattattttaccatttttctgtttacttaataatttgttgtggtattttttgagcttcaggcattt

- - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA