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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttatatgttctttgtatttgtcaaaaccttttcttatcaattcatgtaatgctttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGCTATCAAGAAAATT

Basic information

species Glycine max
transcript GLYMA02G04320.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04320.3 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 5
--ttcttatatgttctttgtattt--gtcaaaaccttttcttatcaattcatgtaatgctttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGCTATCAAGAAAATT
  |||||     ||||||   |||   |||     ||| | ||  |||  |     |    ||| || ||  |||    |  | ||    ||  | ||   ||||||  |||||||||||| || || || |||||||||||||| ||||||||||||||||  ||  |||  ||  || |  |||||||||  || || || |
atttcttcccctttcttttattttcaatcatgctgtttgcataaaaatgtagcatttatactatctgtattcagctttgatgttat----tttttcttccatagGTTCGAGCAATGGTGATTATCAACCCAGGAAACCCTACTGGCCAATGCCTTAGTGAAGGAAACATAAAGGAACTTCTCAAATTCTGCTTCCATGAGAACT

upper sequence: GLYMA02G04320.3 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 6
ttcttatatgttctttgtatttgtcaaaaccttttcttatcaattcatgta-atgc-tttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGCTATCAAGAAAATT
 | |  |     ||||||     |      |   |  | |  || ||| |  |||| || |||    |      |      |         |   ||  ||||||  ||| | |||||| |||||||| ||||| || ||||| || |||||||||||||| ||| |||| ||  || ||| ||  ||||| || ||||| |
-tgtcgtgaacactttgtgac-atgggcttcaaataatgtacatacatatgtatgcattcattccgctctgatcatttcccccccttacctacgatgcttagGTTCGAGCGACGGTGATTATAAATCCAGGAAATCCCACTGGCCAGTGCCTTAGTGAAGCAAATATAAGGGAACTTGTGCGATATTGCTACCATGAAAACT
















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|20497753|gb|BQ272683.1|BQ272683
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|5606534|gb|AI900632.1|AI900632
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|15204829|gb|BI427597.1|BI427597
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|17518503|gb|BM187545.1|BM187545
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|13125648|gb|BG316218.1|BG316218
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|20498019|gb|BQ272949.1|BQ272949
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|14999822|gb|BI320636.1|BI320636
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|22525213|gb|BU084024.1|BU084024
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|120534088|gb|EH262221.1|EH262221
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|22522320|gb|BU081131.1|BU081131
EST:     CAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: CAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|120529217|gb|EH257351.1|EH257351
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|31561742|gb|CD487580.1|CD487580
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|120530295|gb|EH258429.1|EH258429
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|22525567|gb|BU084378.1|BU084378
EST:     AAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: AAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|37996526|gb|CF808115.1|CF808115
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|23064220|gb|BU578993.1|BU578993
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|13562529|gb|BG550749.1|BG550749
EST:     TTAATGAACTTCGTCAATCAGNTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|17519349|gb|BM188391.1|BM188391
EST:     CTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: CTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|120495797|gb|EH223964.1|EH223964
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATA-CT                         GTTAAAGCAATGGTGATCATAAATC-TGGAAACC
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACC
EST: gi|20448749|gb|BQ252873.1|BQ252873
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|192313436|gb|FK005516.1|FK005516
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|7326948|gb|AW620746.1|AW620746
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|17400294|gb|BM177076.1|BM177076
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|6566266|gb|AW233945.1|AW233945
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|120531769|gb|EH259902.1|EH259902
EST:     TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|22522287|gb|BU081107.1|BU081107
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAACAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtaatgctttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGCTATCAAGAAAATT
                                       atttaat  putative branch site (score: 4)
                          aacaaaatcataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttatatgttctttgtatttgtcaaaaccttttcttatcaattcatgtaatgctttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGCTATCAAGAAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA