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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatctgaattttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC

Basic information

species Glycine max
transcript GLYMA03G33830.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33830.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 6
gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatctgaattttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC
                                                                 | |   || | |                ||  |  ||||||   ||  |   | |   |||    | | ||||  |||||||||| |||||||| || || || || |||||||||||||| |||||||||||  | ||| |||| || ||||| ||||||          
----------------------------------------------------------------gtttgaccatatcttgtgttttctttttgatatc--cttgttggtaccctacaaac-atattgcgcttgtagGGAGCTGGTTTGGTGGTTCATGACGCAGGAGCCTACTGCATGAGCATGGCTTCAACCTACAACTTGAAGTTGCGACCACCTGAATATTGG----------

upper sequence: GLYMA03G33830.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G090722_T02 (Zea mays), 3'ss of exon 6
gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatc----tgaattttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC
                                                                   | | |||| |||| | |         |||   |   ||||   |||| || |     |  ||| |  | | ||||  ||||  |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| || |||| || ||||| |||          
---------------------------------------------------------------gtctttttcaaagccactatattttatttgatgattagc-gtttcctctgtttcgttgtgatatattgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCGCCAGAGTACTGG----------

upper sequence: GLYMA03G33830.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatctga---attttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC
                                                                     | |||| |||  | |         |||   |    ||  |  | |||  |||||    || |  | | ||||  ||||  |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| || |||| || || || |||          
---------------------------------------------------------------gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctt-tctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG----------

upper sequence: GLYMA03G33830.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G14390.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatctgaattttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC
                                          || ||||  ||||      ||  ||| || ||   || |           ||||   | |  | | |  |   |        | || ||  |||||  ||||| |||| |||||||| |||||||| || || ||||||||||| || || |||||||| |||||||| ||||| || || |||          
----------------------------------------gtatgataaggatatg-----attctgtttggaagctcagg----------taatgtggaatcttatgagtttatt-------gtattcattacagGGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGCATGGCTTCCACTTACAATCTCAAGATGCGTCCTCCGGAATACTGG----------

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|193482793|gb|FK444028.1|FK444028
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGG
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGG
EST: gi|208084558|gb|GD879748.1|GD879748
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTG
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTG
EST: gi|193696493|gb|FK640211.1|FK640211
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGGTACTGGTTTGGTTGTTCNTGATGCTGGTGCTTA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGG-TACTGGTTTGGTTGTTCATGATGCTGGTGCTTA
EST: gi|298183270|gb|HO028483.1|HO028483
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|208074477|gb|GD868226.1|GD868226
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGT-CTGGTTTGGTTGTTCATGATGCTGGTGCTTA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTA
EST: gi|193340317|gb|FK308232.1|FK308232
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGC-
EST: gi|11274749|gb|BF325084.1|BF325084
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193415754|gb|FK377536.1|FK377536
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193321071|gb|FK287740.1|FK287740
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|11413960|gb|BF426035.1|BF426035
EST:     AGTCTGCAGATTTCTTAAGAAAAAGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGAAGCTGG
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGG
EST: gi|193719674|gb|FK652256.1|FK652256
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTACCTACTCCAGCCAAGgtaatatata ... ttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaagacaacaatgccaacttgtttaaactgtctcatctgaattttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC
                                           ttttaat  putative branch site (score: 3)
                                    atctgaattttaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatctgaattttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG