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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGGGGAAATCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttataattttgttgtttaagcctctaattaagtgtgtgttttggatgaacttttacaaaatttattgaaaatgatgtgatttatgtttgtatga...

Basic information

species Glycine max
transcript GLYMA11G19120.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g06490.1 (Oryza sativa), 5'ss of exon 2
GACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGGGGAAATCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttataattttgttgtttaagcctcta--attaagtgtgtgttttggatgaacttttacaaaatttattgaaaatgatgtgatttatgtttgtatga--
|    || |||| ||| ||| |  ||||||| || ||||||||||| ||||| || |||||||| ||||| || ||||| || ||||| || || |||||||| ||| ||  | || |  |||      ||   | ||  ||  |  || |   |  |||| |||    | || |||   | || |   |  ||| |  | |  
GGAAGCCATGGAAAGCCTTCCTCCTGTACGGGCCACCGGGGACGGGCAAATCTTACTTGGCCAAAGCCGTCGCGACAGAGGCCGATTCCACATTCTTCAGgta-attgattttcttctcatttcttgtactggtactagttgattagttagtgggttctttcacatttgtgatcgaattggttgcg---tgcgttcgattcatt

upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 2
GACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGGGGAAATCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttataattttgt-tgtttaagcctctaattaagtgtgtgttttggatgaactttta-caaaatttattgaaaatgatgtgat-ttatgtttgtatga
|||| ||||||||||| ||  ||||||| || || || || || || |||||||||||||| ||||| |||||||| |||||||| ||||| ||||| ||||| |  |||  ||     ||||| |   ||| |     | |  |    |||||   |  |  |  || |  || |  ||    |||    ||  |   ||  
GACGGCCTTGGAGAGCTTTTCTGTTGTATGGGCCTCCTGGAACAGGAAAATCGTATTTGGCTAAGGCTGTTGCCACTGAAGCTGACTCTACCTTTTTTAGgta-acgtatgtttaaaagtgtttgaatttctgaaagtatataggaagaggatggtgtagtgtcttaactctttcattatagcttgagaccatagtcaaat--
















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|193486744|gb|FK448379.1|FK448379
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTT-CAG                         TATTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|254343324|gb|GR857028.1|GR857028
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|193707983|gb|FK642403.1|FK642403
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAA
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAA
EST: gi|6482719|gb|AW201948.1|AW201948
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCCTGGTTCCAAAGTGGATGGGAGAAAGTGAAAAGC
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACC-TGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGC
EST: gi|207760478|gb|GD734501.1|GD734501
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|193554963|gb|FK514694.1|FK514694
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAA-GCT
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|207710914|gb|GD693992.1|GD693992
EST:     GTATTTTGGTCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: GTA-TTTGG-CCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|207837705|gb|GD810725.1|GD810725
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|9565843|gb|BE475352.1|BE475352
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|208280166|gb|GE075464.1|GE075464
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATG
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATG
EST: gi|193661362|gb|FK601700.1|FK601700
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|208318846|gb|GE111537.1|GE111537
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGA
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGA
EST: gi|24137035|gb|BU927545.1|BU927545
EST:     ACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: ACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|193519014|gb|FK475801.1|FK475801
EST:     CGTATTTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: CGTA-TTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|208105553|gb|GD904648.1|GD904648
EST:     TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAA
genomic: TCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAA
EST: gi|207750339|gb|GD722934.1|GD722934
EST:     CGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAG                         TGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: CGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|193539064|gb|FK496424.1|FK496424
EST:     GTATTTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGC
genomic: GTA-TTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACG-TTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGC
EST: gi|208033100|gb|GD828673.1|GD828673
EST:     CGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: CGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTC-TACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
EST: gi|17023275|gb|BM094309.1|BM094309
EST:     TGATTCTACGTTTTTCAG                         TGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT
genomic: TGATTCTACGTTTTTCAGgtagatttat ... tcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGGGGAAATCGTATTTGGCCAAGGCCGTTGCCACAGAAGCTGATTCTACGTTTTTCAGgtagatttataattttgttgtttaagcctctaattaagtgtgtgttttggatgaacttttacaaaatttattgaaaatgatgtgatttatgtttgtatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT