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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatcattatataattaattccatctactttttcttttcactcatggaaattaatcattgttttgaaactcaattaccaatcaataatatatacatgccattaattttttggctattctaattaatgtgttggcgcgcatctttttatgtactttcag

Basic information

species Glycine max
transcript GLYMA10G32340.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32340.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 5'ss of exon 4
GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatcattatataattaattccatctactttttcttttcactca--tggaaattaatcattgttttga---aactcaattaccaatcaataatatatacatgccat-taattttttggctattctaattaatgtgttggcgcgcatctttttatgtactttcag
|||||||||||  ||||||||||||||  | |||||||| ||||||||||| ||||||||||||  |      |  |   ||| ||| |  |||   ||   | |  |    | ||  ||||     | ||| |   || |    || || | | | | | |    ||  || |||| | ||   | || | | |  ||| |  |                         
GATGTTTGTTGAATCATGCAAGCGCCTTAGGATAATGAAAGGATCAGAAGCTATTGGCCTTGgtcagtgcatatcaagttttatttctacatacaaattagctcctttgggtttgattttaagttggggtttaatttaagttggatatcagttactgacagaacagtgaaatataatatattttttgttttgaat--tgtttcag-------------------------

upper sequence: GLYMA10G32340.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G138268_T01 (Zea mays), 5'ss of exon 4
GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatcattatataattaattccatctactttttcttttcactcatggaaattaatcattgttttga--aactcaattaccaatcaataatatatacatgccattaattttttggctattctaattaatgtgttggcgcgcatctttttatgtactttcag
|||||| || |  |||||||||||||| || || ||||| ||||||||||| |||||||| |||  |      ||||| |||| |   || ||||  | ||   ||   |  || | |    |  ||  | |  | | |  ||     |  ||    | |  ||  | | ||||||   |                                              
GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGGgtgagttgacatatatgattattattat-tactaat-ctcaacaacaaaagagactttctagggtagtaagcagcccgtttgt---ttcatctggtctctatctc-tgaattttccag----------------------------------------------

upper sequence: GLYMA10G32340.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G138268_T02 (Zea mays), 5'ss of exon 3
--------------------------------------GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatcattatataattaattccatctactttttcttttcactcatggaaattaatcattgttttga--aactcaattaccaatcaataatatatacatgccattaattttttggctattctaattaatgtgttggcgcgcatctttttatgtactttcag
                                      |||||| || |  |||||||||||||| || || ||||| ||||||||||| |||||||| |||  |      ||||| |||| |   || ||||  | ||   ||   |  || | |    |  ||  | |  | | |  ||     |  ||    | |  ||  | | ||||||   |                                              
TAATCGGAAAATAATAATAATTTCCATTTCATTTTCAGGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGGgtgagttgacatatatgattattattat-tactaat-ctcaacaacaaaagagactttctagggtagtaagcagcccgtttgt---ttcatctggtctctatctc-tgaattttccag----------------------------------------------

upper sequence: GLYMA10G32340.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatcattatataattaattccatctactttttcttttcac---tcatgga-aattaatcattgttt-tgaaactcaattaccaa-tcaataatatatacatgccatt--aattttttggctattctaattaatgtg-ttggcgcgcatctttttatgtactttcag--------------------
|||||||||||  |||||||||||| |||| |||||||| ||||||||||| ||||| ||||||| |||  |||    |         || |   |   |||   ||   ||||| | |||  ||||| |    |    |   || | ||  ||||   |||||  ||  || |  ||  ||||   |||| | |||||| |  ||  |    || |   ||| ||  |   |                    
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagca--attgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag

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|192319925|gb|FK012973.1|FK012973
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|14991595|gb|BI317268.1|BI317268
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
EST: gi|12687908|gb|BG154304.1|BG154304
EST:     GTCATGCANGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|209714040|gb|BW684491.1|BW684491
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAAGCAGAAGCTGAAGCTGGCCTAAT
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGC-AAAAGCAGAAGCTGAAGCTGGCCTAAT
EST: gi|192322219|gb|FK014115.1|FK014115
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|31465555|gb|CD407583.1|CD407583
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|19269830|gb|BM886086.1|BM886086
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|31306889|gb|CD392092.1|CD392092
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|10233565|gb|BE802453.1|BE802453
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
EST: gi|19053573|gb|BM732240.1|BM732240
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|41145593|gb|CK605804.1|CK605804
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGTAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|4292511|gb|AI441915.1|AI441915
EST:     GTCATGCAAACACCTGCAAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|15661889|gb|BI699260.1|BI699260
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|37997457|gb|CF809046.1|CF809046
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|15815503|gb|BI787778.1|BI787778
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|192319926|gb|FK012974.1|FK012974
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|26269385|gb|CA820448.1|CA820448
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|7286253|gb|AW598740.1|AW598740
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|9258968|gb|BE347115.1|BE347115
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|31459036|gb|CD401064.1|CD401064
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGATAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
EST: gi|10844620|gb|BF067790.1|BF067790
EST:     GTCAN-CAAGCGCCTGCCA-TAATGAAGGGATCAGAAGCGATTGGCCTTG                         CTCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTG
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTG
EST: gi|31460983|gb|CD403011.1|CD403011
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatcattatataattaattccatctactttttcttttcactcatggaaattaatcattgttttgaaactcaattaccaatcaataatatatacatgccattaattttttggctattctaattaatgtgttggcgcgcatctttttatgtactttcag

- - - - - - - - - - - - - - - - - - - - - -  AGAAGC