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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC

Basic information

species Glycine max
transcript GLYMA11G10770.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 2
aattttgtaatttgattggttatcttttcatagatatgga---ttttgctatgatag-agtatgag--------aacaaatatcgctttactgaaaatagcaatatatgt-agGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
             ||  | || | |||||| | | |  ||    |     ||  ||| ||||  |         ||    |  | || | || |   | | |  || | | |||||||||||| || |||||||| ||||||||||||||||| ||||| ||||||||||||||  |||||||||| || || ||||||||||||||||| ||
-------------gagagatttttttttcaaaaaaacagagaactcgagcatattagtagtacaaatccttctcaattgctgccactcttctaatgtttgtatgatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
aattttgtaatttgattggttatcttttcatagatatggattttgctatgat----agagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
     ||  | |   |||    |  |     | || |  | | |   |  |     ||  |||   | ||   |     | |||      |    | | |  ||||||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||| |||||| ||||||||||||| || || || ||||||||||| ||
--aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatt--tttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 2
aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgcttta-ctgaaaat----agcaatata----tgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
    ||||  |||| | |  |   | |||| ||| ||| |      ||  |   |   |     ||  |  | || || ||| || |    | || || |    | ||||||||||||| || |||||||| ||||||||||| ||||| ||||||||||||||||| ||  | |||||||| || || |||||||||||||| || ||
----ttgttgtttggtagcct--ttattcaaaga-atgaaaaca--taaaaggaacctttttgtcagtttgctctctaactgtaagttttaatcactacaattttttagGTAAAAGGGCATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCGAAGGCACTTGCTGCGGCTGGTGCTGAAATTCTTGTGGGTAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G079256_T01 (Zea mays), 3'ss of exon 2
aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaat-------atatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
      |||  |    |||  || ||||  ||  |||||  | ||   | ||  |       || || |     ||| | || |  |   ||        | |  ||||||||| || ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| ||  |||||||||| || || ||||| ||||||||||| ||
------gtacatgatctggcaattttttt-tatctatgggatctgaactaatgcacatattcaataactgcaagttttcagacatcaattatcttgcaagttttcagGTAAAAGAGCATTTATAGCTGGAGTTGCTGATGATAATGGTTATGGTTGGGCAATTGCTAAGGCTCTTGCTGCTGCTGGTGCTGAGATTCTTGTTGGTAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
aattttgtaatttgattggt-tatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
           ||| ||||  |||||||   |  ||   ||     || || |    | ||| |  ||  |       | || |||| | |        ||| ||||| ||||| ||||||||| | |||||||| ||||| ||||| ||||| || ||||||||||||||||| || |||||||||||  | ||||| ||
----------gttggttggcatatctttctttgaattcagagaagact-tggtgctatctga-actaagca-------agtgtaaatggta-------cagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaat----atatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
   ||||| |||| |    | |  | ||  |     ||  | ||| || || | |  |  |  |  | || | ||| |   ||||  |  ||    || ||||||||| || || ||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||| || || || ||||||||||||||||||||
--gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaa--aataagattacctcttcaactaaaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 2
-aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
  |  |   ||  ||         ||    | ||  || | ||||      |  |  |     | || ||     ||||||  || | | | | |  ||||| ||||| || |||||||| ||||| || |||||| | || | ||| ||||| ||||| ||| |||| || ||||| ||||||||||||||||| || ||
gtacctgacaa--tggcgcagcgactaagtagag-catagcttttttaggaaccgcttgctgtaccacatgctcatttacttcaatttgtatttt--gtagGGAAAAGAGCGTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10940 (Selaginella moellendorffii), 3'ss of exon 1
aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
                                  |||   || |   |||   |  | || |||      |    || ||     |        ||| ||| || ||||| ||||| ||||| || || |||||  | |||||||||||||| ||||| ||| | |||||| | ||||| |||||||||||  | || ||
---------------------------------gtatttcttctttcatgcatgcat-tgtgaattttccttttgttgctcgtgtttctgtcgcatgcagGGAAGAGGGCATTTATCGCTGGAGTGGCCGATGATCAAGGATATGGATGGGCGATTGCCAAAACGCTTGCTTCTGCCGGGGCTGAAATTCTCTTGGGAAC

upper sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ25882 (Selaginella moellendorffii), 3'ss of exon 1
aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
                                  |||   || |   |||   |  | ||   |      |    || ||     |        ||| ||| || ||||| ||||| ||||| || || |||||  | |||||||||||||| ||||| ||| | |||||| | ||||| ||||||||||| || || ||
---------------------------------gtatttcttctttcatgcgtgcat-tgtagattttccttttgttgctcgtgtttctgtcgcatgcagGGAAGAGGGCATTTATCGCTGGAGTGGCCGATGATCAAGGATATGGATGGGCGATTGCCAAAACGCTTGCTTCTGCCGGGGCTGAAATTCTCGTGGGAAC

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|18039953|gb|BM308247.1|BM308247
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGAC
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGAC
EST: gi|298166168|gb|HO009139.1|HO009139
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
EST: gi|7796132|gb|AW781529.1|AW781529
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTNTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
EST: gi|192307619|gb|FG999658.1|FG999658
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
EST: gi|209721947|gb|BW680082.1|BW680082
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
EST: gi|7796512|gb|AW781909.1|AW781909
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
EST: gi|208239696|gb|GE039174.1|GE039174
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTG
EST: gi|7041859|gb|AW471753.1|AW471753
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
EST: gi|298168738|gb|HO009668.1|HO009668
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
EST: gi|192306220|gb|FG995056.1|FG995056
EST:     TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAG                         GTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG
genomic: TGAGTCCAGTGCACAAAGTGCAGTCTCAGGATTGCCAATTAATCTGAAAGgtattgttca ... atatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC
                                    aaaatagcaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattttgtaatttgattggttatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA