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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCATCCTTGCCTGAAAATGATTGCCGATACGCTGTCTTTGACTTTGATTTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcacttagtttcttgtacaaccatagaattgcatattgtattaactcattgatttctgtatacactgttttacatgtgtgaatatattgcacttg...

Basic information

species Glycine max
transcript GLYMA20G35190.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35190.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G31200.1 (Arabidopsis thaliana), 5'ss of exon 2
CTGCATCCTTGCCTGAAAATGATTGCCGATACGCTGTCTTTGACTTTGATTTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcacttagtttcttgtacaaccatagaattgcatattgtattaactcattgatttctgtatacactgttttacatgtgtgaatatattgcacttg
  || ||  | ||||| ||||| ||| |||||||||| | |||||||||||| || || |||||||| || ||||||||||||||||| ||  |||| ||||||||   ||  ||| |   || |  |   | |     |  || || |    ||||       | |   || |||     |    || |  |       
TAGCTTCACTTCCTGATAATGACTGCAGATACGCTGTTTATGACTTTGATTTCGTTACTTCTGAGAATTGTCAAAAGAGCAAAATCTTCTTCTTTGCTTGgttagt---ttgattttt---accattagtaagtctataagggttttgatgtgttgagactaaaacattttgatttgggactactgatgttgtag-----

upper sequence: GLYMA20G35190.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0049g00980.t01 (Vitis vinifera), 5'ss of exon 2
CTGCATCCTTGCCTGAAAATGATTGCCGATACGCTGTCTTTGACTTTGATTTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcacttagtttcttgtacaaccatagaattgcatattgtattaactcattgatttctgtatacactgttttacatgtgtgaatatattgcacttg----
|||| ||||| ||||| ||||||||||| || ||  | | ||||||||||||||| || ||||||||||||||||||||||| || || || ||||||||||  ||  |||  |    || |  |   || |  ||   |||||| || ||  || | |       ||      |||  |||  || | |       ||     
CTGCTTCCTTACCTGAGAATGATTGCCGCTATGCAATTTATGACTTTGATTTTGTTACTTCTGAGAACTGCCAAAAGAGCAAGATATTCTTCATTGCATGgtgtgtttctttttgaactg-atcattttacatatg---attgtagtagctgtttaaatcaaaagcacttctccttagttgttcgagtcttgcctcattatatt
















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|209714633|gb|BW654045.1|BW654045
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|21887631|gb|BQ740844.1|BQ740844
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|209718314|gb|BW677577.1|BW677577
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|254336711|gb|GR842890.1|GR842890
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|254334310|gb|GR844095.1|GR844095
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|7796710|gb|AW782104.1|AW782104
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|213614378|gb|DB976443.1|DB976443
EST:     TTGTGACATAAGAGAACTGCCAAAAGAGCAAAATCTTTCTGAATGCATCT                         G-CTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCA
genomic: TTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCAT-Ggttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCA
EST: gi|120529277|gb|EH257411.1|EH257411
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|6719559|gb|AW307206.1|AW307206
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|15814871|gb|BI787146.1|BI787146
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|10256154|gb|BE823920.1|BE823920
EST:     TTTGTGACANNNGAGNNCTGCCAAAAGAGCAAAANCTTTTTTATTGCATG                         GNCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|254336712|gb|GR842891.1|GR842891
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|7925293|gb|AW831319.1|AW831319
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|31476399|gb|CD418427.1|CD418427
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|14258838|gb|BG881746.1|BG881746
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|57574434|gb|CX547409.1|CX547409
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|21993856|gb|BQ785384.1|BQ785384
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
EST: gi|120529143|gb|EH257277.1|EH257277
EST:     TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATG                         GTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA
genomic: TTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcact ... tattttacagGTCTCCTTCAGTGGCCCGCATTCGCCCGAAGATGCTATATGCAACATCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCATCCTTGCCTGAAAATGATTGCCGATACGCTGTCTTTGACTTTGATTTTGTGACATCTGAGAACTGCCAAAAGAGCAAAATCTTTTTTATTGCATGgttagtcacttagtttcttgtacaaccatagaattgcatattgtattaactcattgatttctgtatacactgttttacatgtgtgaatatattgcacttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA