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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG

Basic information

species Glycine max
transcript GLYMA14G40320.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 10
gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG
         ||  |   ||  |||| ||   ||  | |   |||     ||||  | | || |||   | ||   |   |  |   ||      ||||||| || || || ||||| ||||| || |||||||||||||||||||| ||||||||||| || |||||||| |||||||||||||| ||  | ||||
---------gtactagattactatttcatg-aacgacacggtattccattcat--tgacttatgcagcctaaaccta--taagctattatctgtagGGTCTCGTCGACTCGGACACATTGCCTCTCAATGTATCACGAGAAATGCTCCAACAACATAGCAGCCTGAAGACCATCAAGAAGAAACTAATCCGCAAAG

upper sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG
         ||  |   ||| || | ||     | ||||   || |   | | |   || | |  ||  |||| || |  | ||  ||      ||||| ||||||| || |||||  |||| || ||||| |||||||||||||| ||||||||||| ||||||||||| ||||||||||| || ||  | ||||
---------gtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagt-gatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG

upper sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataattt--ttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG
         ||  ||  ||  | || ||   |||    |  |||     |||   | || |  | ||   | ||   ||    ||   ||      ||||| ||||||| || |||||  |||| || || || |||||||||||||||||||||||||| ||||| ||||| ||||||||||| || ||  | ||||
---------gtactgtattactgtttcaag-aaacgcgtactattcaattcaatctgatgtcatagcaggctaaaccttacagtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG

upper sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttttgacgttggga--acagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG
         ||       |   |   || |  ||    || | | |     |||  ||||| ||     ||||   |    ||| ||||      |||||||||||||| |||||||| ||||| || ||||||||| ||||||||||||||||||| || ||  | |||||||| |||||||| |||||  | || |
---------gtaaactacttgaaagacaaactaaggggttctttca-----atacaaatttatgg-gctaaatccctaacgtga-gttgcttttgcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAATGCTTCAACAACACAGCAGCTTAAAGACAATTAAGAAGAAGCTTATCCGAAAGG

upper sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
---gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttt-----tgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG
    ||       || |   ||  |||||  | |   | ||   |  ||| ||  | || | ||  | | | || || ||||       |||||||  || ||||||||||| ||||| ||||| || || |||||||| ||||||||||||||||||||||| || ||| |||| ||||| |||||||| |||||  | || |
gttataaatcaatttataaattcctattg--ggttcttgtaaactg-gagaat--ttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG

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|298169805|gb|HO018429.1|HO018429
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|57574607|gb|CX547582.1|CX547582
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|208064687|gb|GD865067.1|GD865067
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|8283891|gb|BE021450.1|BE021450
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTNTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|15661681|gb|BI699052.1|BI699052
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|192301679|gb|FG997621.1|FG997621
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|192313365|gb|FK005137.1|FK005137
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|58019806|gb|CX706548.1|CX706548
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|208331878|gb|GE130701.1|GE130701
EST:     TTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATT
EST: gi|192313364|gb|FK005136.1|FK005136
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|192309871|gb|FK001415.1|FK001415
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|208262509|gb|GE059268.1|GE059268
EST:     TGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|23059035|gb|BU578351.1|BU578351
EST:     TTTCAGATGATTTTATTGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|7233546|gb|AW568951.1|AW568951
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
EST: gi|213592217|gb|DB965980.1|DB965980
EST:     TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTG                         GGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattg ... ttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaggatcataataatttttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG
          ataataatttttgcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA