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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacttattttaacttcgttatatgattaccatatatgttcatgatgcgtattaattgatcataatatataaagtgatattgatgagttgaaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTGGCTGTGCAAAAGAGCGTTGGAGAAGAGAGCGAGAAGAACAGCAGCCCT

Basic information

species Glycine max
transcript GLYMA19G34380.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
--taacttattttaacttcgttatatgattaccatatatgttcatgatgcgtattaattga-tcataatatataaagtgatattgatgagttgaaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTGGCTGTGCAAAAGAGCGTTGGAGAAGAGAGCGAGAAGAACAGCAGCCCT
   ||  || |      ||   ||     |  ||      |  |   || |||    |||| |  | | | |   ||  ||||||     |  | |  || ||| | ||||||||||| |||||||| || ||||| ||||||||||||||  || | |||||      |   || |  |    ||  ||   |  ||   | 
ataaatctaatgctggatctggatggacgtctcagtctcatctaccgtgtgtacgttttgagttttgacagagggaggtatattgt---atatacacctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC

upper sequence: GLYMA19G34380.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0141g00290.t01 (Vitis vinifera), 3'ss of exon 1
taacttattttaacttcgttatatgattaccata-tatgttcatgatgcgtattaattgatcataatatataaagtgat--attgatg--agttgaaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTGGCTGTGCAAAAGAGCGTTGGAGAAGAGAGCGAGAAGAACAGCAGCCCT
    || ||     |        |  ||  |||| ||   |||| |     |   ||  || | |||| |  | ||||   ||| |||  | ||| ||| | |||| | ||||| ||||| |||||||| || |||||||||||||||||||||||||| | ||| ||| |||   | || ||  | ||||||   ||| ||   
----tttttcctgttaaaaacagttgttctcataataaagtcattaactaaaaccatacataaaaataaagcaggtgaataattcatggaaattggaattt-tagGGCACAGGTTGTGGGGTGGCCACCGGTTCGGTCCTTCCGGAAGAACATGTTGGCCGGGCAGAAGGGCGGCAGCGAGGAAGGGGAGAAGGTGAGCTGCAAC
















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|9440021|gb|BE440532.1|BE440532
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|151405703|gb|EV275517.1|EV275517
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|16346301|gb|BI971896.1|BI971896
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|7795391|gb|AW780716.1|AW780716
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGT-GGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|151412951|gb|EV282763.1|EV282763
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|9204440|gb|BE330664.1|BE330664
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|213600363|gb|DB970299.1|DB970299
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|209707048|gb|BW661554.1|BW661554
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|209700152|gb|BW656269.1|BW656269
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|14126638|gb|BG791076.1|BG791076
EST:     CCTGAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|151409764|gb|EV279572.1|EV279572
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|209706317|gb|BW676305.1|BW676305
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|12772578|gb|BG237569.1|BG237569
EST:     TTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: TTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|213611837|gb|DB960681.1|DB960681
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|192303186|gb|FG997762.1|FG997762
EST:     CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAA                         GACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACCCTTCTGCCAGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttact ... aaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgtattaattgatcataatatataaagtgatattgatgagttgaaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTGGCTGTGCAAAAGAGCGTTGGAGAAGAGAGCGAGAAGAACAGCAGCCCT
     attaattgatcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacttattttaacttcgttatatgattaccatatatgttcatgatgcgtattaattgatcataatatataaagtgatattgatgagttgaaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTGGCTGTGCAAAAGAGCGTTGGAGAAGAGAGCGAGAAGAACAGCAGCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - catgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgag