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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaacttgtcaatcttctgaagctttactcagtaaggaacagctataatcatatttactttttgaaggggtactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCGGCTGCCATAGATGGGCTTCCGGATCCTGGTGGGCCAACAGT

Basic information

species Glycine max
transcript GLYMA10G29810.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29810.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0128g00050.t01 (Vitis vinifera), 3'ss of exon 2
taaaacttgtcaatcttctgaagctt-tactcagtaaggaacagctataatcat--atttactttttga-aggggtactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCGGCTGCCATAGATGGGCTTCCGGATCCTGGTGGGCCAACAGT
      || ||| | ||||  |  |  || | | ||      |  | |  |||   ||| | ||  ||  |   | | ||  |   | ||||| |    |||||| || || || || || ||||||||||||||  |||| |||| ||| |||||||||| ||||||||| ||||| ||||| ||| ||||||| ||| ||||
----gattctcatttttcttgatttgataatgaatagcagtaaattttcctcagcaattgaattcatggtaattggagtatttgattttggttgactactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAACGGCTAGTGGCTGCCATTGATGGCCTTCCAGATGCTGGTGGCCCATCAGT
















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|192295336|gb|FG985990.1|FG985990
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|151394065|gb|EV263936.1|EV263936
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|20498085|gb|BQ273015.1|BQ273015
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|13312736|gb|BG406387.1|BG406387
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|16283740|gb|BI945712.1|BI945712
EST:     AGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|209726122|gb|BW675297.1|BW675297
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|207819086|gb|GD793220.1|GD793220
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|192321485|gb|FK011757.1|FK011757
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTTTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|151406399|gb|EV276214.1|EV276214
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|22928578|gb|BU545717.1|BU545717
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TANNNGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|151393222|gb|EV263097.1|EV263097
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|31469567|gb|CD411595.1|CD411595
EST:     AGCTGTGGGGGTAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|105634314|gb|DW247463.1|DW247463
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAG
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAG
EST: gi|192294333|gb|FG987262.1|FG987262
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatcatatttactttttgaaggggtactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCGGCTGCCATAGATGGGCTTCCGGATCCTGGTGGGCCAACAGT
      atatttactttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaacttgtcaatcttctgaagctttactcagtaaggaacagctataatcatatttactttttgaaggggtactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCGGCTGCCATAGATGGGCTTCCGGATCCTGGTGGGCCAACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - -cttgtca
- - - - - - -tcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtc