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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgattataaaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt...

Basic information

species Glycine max
transcript GLYMA20G32320.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 7
GATGGCACT-GACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgattataaaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt-------
    ||||  || ||||||||||||||| ||||| ||||||| |||||||| ||||||||||| |||||||||||  || | |||||||||||     |    | |       || ||||   | | |   |   || ||       ||  |  |||||  ||| |||       | |  ||| || |       
-GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAGgtatgccccctagcatatga-----agctatttgctttcacgatgtccaagaagcaggatagctaacaaga--gaacatgctattttatttcaaattaatcaagctg

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 8
GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgattataaaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt-
||||     ||||| |||||||||||  ||||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||||||| ||   ||        |    ||| |  || | |      |  |  |    || ||  || |||   | ||  |   |  ||  ||||||| |   
GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttgagtgcatgaaatgtttgttttacataacatgcaagaggagaagcaattctagctg-caactgttaatgttattctactttagaaaagatca

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM5G863105_T01 (Zea mays), 5'ss of exon 3
GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgattata---aaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt
||||     |||||||||||||||||  | ||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||||||| ||    |       ||    ||| |  || | |   ||  | |  |  | || | |       ||  ||||  | | | ||   |  | | |  || 
GATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttgaatacataaactgtttgttttacataacatgtaagatgagaaacaaatctagctgcaaccattaatgctattct-tgtttaa-aaagaccag-

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 7
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 7
GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgatt-ataaaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt-
||||| |  ||   |||||||||||| |  ||||| ||||| ||||| || || |||||||| ||||| |||||| ||||||||||||| ||     |  |||||| | ||   ||  ||||  ||    ||   |    |||||  |        |  ||     | | | |    |    ||| |  
GATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAGgtgtgcac--ttctttcttgcctctgatttatgatcgattttcttgtcctctgcatttattgagatcttattatccgtttctttcattgctttggaattgga

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgattataaaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt-------
||||| | ||| |||||||||||||||| |||||| || || || ||||||||||||||||| ||||| |||||  | ||||||||||||  |       ||| ||  ||   | ||   ||| |     || |  |   |  |||    |   |  ||||  ||  |||||| | |||       |       
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccatttt----ctatttgtaggacattgc---taaaattaatggcaagctgtgaataatagctctagatgaacaaa

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|19937689|gb|BQ081385.1|BQ081385
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|192303626|gb|FG998636.1|FG998636
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|208166021|gb|GD959081.1|GD959081
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGACCCAATCAGTTAGTTGA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCG-CCCA-TCAGTTAGTTGA
EST: gi|207760676|gb|GD733677.1|GD733677
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGA
EST: gi|8670136|gb|BE191243.1|BE191243
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|213611330|gb|DB983950.1|DB983950
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|151401597|gb|EV271411.1|EV271411
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAA-GATTGCCTCGCCCATCAGTTAGTTGATGTAGC-AGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|31307751|gb|CD392954.1|CD392954
EST:     TCATAGAGACATCTGCCAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|8670147|gb|BE191254.1|BE191254
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|58017129|gb|CX703871.1|CX703871
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|193307625|gb|FK270639.1|FK270639
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|208308185|gb|GE102837.1|GE102837
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGA
EST: gi|6667685|gb|AW279136.1|AW279136
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|7589360|gb|AW705136.1|AW705136
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGT
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGATTGCCTCGCCCATCAGTTAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgattataaaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccttcc