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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatcatatatttatcttttgttatatagttgcttacataataataatatacatgcataatctatgcaaaactatgacaaagacaacaatgccaacttgtttaaactatctcatctgaattttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG

Basic information

species Glycine max
transcript GLYMA19G36580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 6
gtaatatcatatatttatcttttgttatatagttgcttacataataataatatacatgcataatctatgcaaaactatgacaaagacaacaatgccaacttgtttaaactatctcatctgaattttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG
                                                               | |   || | ||               ||  |  ||||||   ||  |   | |   |||    |   ||||  |||||||||| |||||||| || || || || |||||||||||||| |||||||||||  | ||| |||| || ||||| ||||||
--------------------------------------------------------------gtttgaccatatcttgtgttttctttttgatatc--cttgttggtaccctacaaac-atattgcgcttgtagGGAGCTGGTTTGGTGGTTCATGACGCAGGAGCCTACTGCATGAGCATGGCTTCAACCTACAACTTGAAGTTGCGACCACCTGAATATTGG

upper sequence: GLYMA19G36580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G090722_T02 (Zea mays), 3'ss of exon 6
gtaatatcatatatttatcttttgttatatagttgcttacataataataatatacatgcataatctatgcaaaactatgacaaagacaacaatgccaacttgtttaaactatctcatc----tgaattttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG
                                                                 | | |||| | |  | |         |||   |   ||||   || | || |     |  ||| |  |   ||||  ||||  |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| || |||| || ||||| |||
-------------------------------------------------------------gtctttttcaaagccactatattttatttgatgattagc-gtttcctctgtttcgttgtgatatattgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCGCCAGAGTACTGG

upper sequence: GLYMA19G36580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
gtaatatcatatatttatcttttgttatatagttgcttacataataataatatacatgcataatctatgcaaaactatgacaaagacaacaatgccaacttgtttaaactatctcatctgaattttaatgtc--agGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG
                                                                   | |||| | || | |         |||   |    ||  |  | |||       || ||    |   ||||  ||||  |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| || |||| || || || |||
-------------------------------------------------------------gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctttctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG

upper sequence: GLYMA19G36580.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G14390.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatatcatatatttatcttttgttatatagttgcttacataataataatatacatgcataatctatg-caaaactatgacaaagacaacaatgccaacttgtttaaactatctcatctgaatttta---atgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG
                                                                 ||||  ||   |||||    |     ||   ||  |  | |  | | |      |  ||| ||   ||  |||||  ||||| |||| |||||||| |||||||| || || ||||||||||| || || |||||||| |||||||| ||||| || || |||
----------------------------------------------------------------gtatgataaggatatgattctgtttggaagctcaggtaatgtggaatcttatgagtttattgtattcattacagGGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGCATGGCTTCCACTTACAATCTCAAGATGCGTCCTCCGGAATACTGG

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|208142531|gb|GD934031.1|GD934031
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCAT
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCAT
EST: gi|193417877|gb|FK384297.1|FK384297
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|209729664|gb|BW669764.1|BW669764
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|209700621|gb|BW670339.1|BW670339
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|207714375|gb|GD696428.1|GD696428
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|31465431|gb|CD407459.1|CD407459
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193318299|gb|FK287501.1|FK287501
EST:     GTCTGCAGATTTCT-AGGAAAAGGAAGAGAACCTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTT
genomic: GTCTGCAGATTTCTTAGGAAAAGGAAGAGAAC-TTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTT
EST: gi|22928652|gb|BU545791.1|BU545791
EST:     AGTCTGCAGATTNNNTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193398255|gb|FK363435.1|FK363435
EST:     AGTCTGCAGATTTCT-AGGAAAAGGA-GAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTT
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTT
EST: gi|209726659|gb|BW666578.1|BW666578
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|151407666|gb|EV277481.1|EV277481
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|192316336|gb|FK011681.1|FK011681
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|26060133|gb|CA803047.1|CA803047
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|207822812|gb|GD794047.1|GD794047
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|214009020|gb|DB987099.1|DB987099
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|298188879|gb|HO035572.1|HO035572
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|18735168|gb|BM528606.1|BM528606
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193386371|gb|FK350375.1|FK350375
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTT
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTT
EST: gi|209726442|gb|BW658049.1|BW658049
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|192333001|gb|FK024650.1|FK024650
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|192296879|gb|FG990240.1|FG990240
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATAGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|208064329|gb|GD866711.1|GD866711
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193401326|gb|FK367539.1|FK367539
EST:     GTCTGCAGATTTCT-AGGAAAAGGA-GAGAACCTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTT
genomic: GTCTGCAGATTTCTTAGGAAAAGGAAGAGAAC-TTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTT
EST: gi|192317325|gb|FK010556.1|FK010556
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|151395109|gb|EV264980.1|EV264980
EST:     AGTCTGCAGATTTCTTAGTAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|207778051|gb|GD747970.1|GD747970
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCA
EST: gi|209711753|gb|BW676892.1|BW676892
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|209711463|gb|BW665215.1|BW665215
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193362479|gb|FK325317.1|FK325317
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
EST: gi|193337950|gb|FK305089.1|FK305089
EST:     AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAG                         GGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA
genomic: AGTCTGCAGATTTCTTAGGAAAAGGAAGAGAACTTCCTACTCCAGCCAAGgtaatatcat ... ttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaagacaacaatgccaacttgtttaaactatctcatctgaattttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG
                                           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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatcatatatttatcttttgttatatagttgcttacataataataatatacatgcataatctatgcaaaactatgacaaagacaacaatgccaacttgtttaaactatctcatctgaattttaatgtcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG

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