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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttacaaatcactaaaggtttctgaacaaataattctttgtaggagagttagtgccatctaattgtatccttaacttggaatgatttctttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG

Basic information

species Glycine max
transcript GLYMA20G35600.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 7
ttttacaaatcactaaaggtttctgaacaaataattctttgtaggagagttagtgcc-atctaattgtatcct--taacttggaatgatttctttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG
   || | ||||    |  ||||||    | |  ||  || || |  | | ||  |  |  |    || |  |  ||  || |    || |   | | | ||||| || || || ||||||| |||||||||||||||||| || |||||||| ||||||
-aatatatatcatatgatctttctgggatatt--ttacttctaagcaaatcagaacttacatggacgtcttttgatacttttgtgaaatgttgatatatttagATTGTCAATGTCCCTGAGAAAGGAGCAAGGAAGCATCCTCGCGGTGATAATATACAG

upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G050186_T05 (Zea mays), 3'ss of exon 7
-ttttacaaatcactaaaggtttctgaacaaataattctttgtaggagagtta-gtgccatctaattgtatccttaacttggaatgatttctttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG
  |||     ||| |   ||| |   || |||| ||   ||||   | | ||   |   |     || | |  ||  | |      |||      ||  ||||| || ||||||||||||| |||||||||||||||||| || |||||||| ||||||
agtttgtct-tcattgggggtataacaa-aaattataacttgtttcatatttctatataaatgttttatttatttttccttttgaaattatggcatgcttagATAGTCAACGTTCCTGAGAAAGGAGCAAGGAAGCATCCTCGTGGTGATAATATACAG

upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G101791_T02 (Zea mays), 3'ss of exon 7
ttttacaaatcactaaaggtttctgaacaaataattctttgtaggagagttagtgccatctaattgtatccttaacttggaat----gatttctttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG
 |       ||   |  ||    |  | || | ||   ||||   | |  |    | || ||| |||||  |||| |     |     |||   |  ||  ||||| || ||||||||||| | |||||||||||||||||| || |||||||| ||||||
atcagtttgtcttcattggggcatacaaaagttatagcttgtttcatatct----ctatataaatgtattattaattctccgtttcaaattctgtcatgcttagATAGTCAACGTTCCTGAAAAAGGAGCAAGGAAGCATCCTCGTGGTGATAATATACAG

upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 7
ttttacaaatcactaaaggtttctgaacaaataattct-ttgtaggagagttag--tgccatctaattgtatccttaacttggaatgatttctttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG
    |   || |       |||   | ||   |   || || ||  |   || |     | | |  | || |||| ||| |  |||| |||  | || || |||| || || ||||||||||  ||||| ||||||||||| ||||||||||| || |||
---aatggattatcttgcttttgaaatcagccatgcctgttatataaccattggatcatcgtttgttggtgtcctgaacgtataatgtttttgtcttctccagATAGTGAATGTTCCTGAGAAGGGAGCGAGGAAGCATCCTCGGGGTGATAATATTCAG

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|193357635|gb|FK320201.1|FK320201
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|208311212|gb|GE102988.1|GE102988
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|193344284|gb|FK312814.1|FK312814
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATT-AAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|193456440|gb|FK421786.1|FK421786
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|193425329|gb|FK388602.1|FK388602
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATTCCACGGGGTGATAA
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCA-TCCACGGGGTGATAA
EST: gi|17519864|gb|BM188906.1|BM188906
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|193354939|gb|FK322548.1|FK322548
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|193339490|gb|FK302737.1|FK302737
EST:     GCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: GCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|207809763|gb|GD781837.1|GD781837
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|193361573|gb|FK324355.1|FK324355
EST:     TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
EST: gi|193400816|gb|FK368737.1|FK368737
EST:     TTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAAATGCTGGAAGGAACT                         ATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC
genomic: TTCTGGTGAGGGTGTTCAGCAGGCATTATT-AAAAATGCTGGAAGGAACTgtaagtaaaa ... ttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttagtgccatctaattgtatccttaacttggaatgatttctttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG
                        ccttaac  putative branch site (score: 3)
                                        tttctttttgtct  putative PPT
                                   aatgatttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttacaaatcactaaaggtttctgaacaaataattctttgtaggagagttagtgccatctaattgtatccttaacttggaatgatttctttttgtctagATGGTAAACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaatga