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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtactatgttatttgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaatatcaacttcatagcttaaatattagttt...

Basic information

species Zea mays
transcript GRMZM2G038791_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 5'ss of exon 5
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtactatgttatttgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaatatcaacttcatagcttaaatattagttt--
||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||| |||||||||||||| ||||| ||||| || ||||||||||      |  |   ||  | | ||| ||||  ||  ||   |  || ||| |  ||| | ||| |  | |  |   |        |  |  | |  
TGTTGGAGGTGTTGCCAGGGCACGTGCTTTTGCCAAAAAGCTATCAGATGCACCTCTAGCAATTGTTGATAAAAGAAGGCATGGACACAATGTTGCCGAGgcaagtagagcattctttgctttctggtttatacaggataaacattta--tgaatgcaagtaggaaaaataacttagttcgttctaagttcttctgatcttc

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G24280.2 (Glycine max), 5'ss of exon 5
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtactatgttatttg--cttaaacagtgtagccagccaaatggatgtatatagaagaaaaatatcaacttcat--agcttaaatattagttt
|||||| ||||||||||| |||||||| |||||||||||  | || ||||| ||| |||||||||| ||||||||  | || || |||||||| ||||||| | |  |  | |||   |    |||   | |    | | ||      || ||  |  ||   | || || | | |    |  ||  |  | ||||||      
TGTTGGTGGTGTTGCCAGAGCACGTGCTTTTGCCAAAAAATTATCTGATGCTCCTTTAGCTATTGTTGATAAAAGGCGCCATGGGCATAATGTTGCTGAGgtatgattcttcgtaagtttgagtttagacgtctcaattataatggttcagattcaattactcaaaataagactcttggttgtatgaaattgaaatatac----

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G12660.1 (Glycine max), 5'ss of exon 5
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtac-tatg---ttatttgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaatatcaacttcatagcttaaatattagttt
|||||| ||||||||||| |||||||| ||||| |||||  | || ||||| ||| |||||||||| ||||||||  | || || |||||||| ||||||| | |  |  |  ||  | ||   |||  ||  ||||   | ||      || ||  |  |    | || || | | | |     ||     | | |  | |  
TGTTGGTGGTGTTGCCAGAGCACGTGCTTTTGCTAAAAAATTATCTGATGCTCCTTTAGCTATTGTTGATAAAAGGCGCCATGGGCATAATGTTGCTGAGgtatgattcttcatatgtttgagtttagatgtctaaat--tataatggttcagattcaattgctcaaaataagactcttagtagtatgaaacatacaaaatt--

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G16400.3 (Glycine max), 5'ss of exon 5
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgta----ctatgttatttgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaatatcaacttcatagcttaaatattagttt
|||||| |||||||| || |||||||| ||||| || ||  | || ||||||||| ||||||||||||| || ||  | || ||||| ||||| ||||||| ||  |       |    ||   || | | ||| ||  |   |  |   |   |   |  || ||    | | |   |   |  | || ||   |||| |   
TGTTGGTGGTGTTGCAAGAGCACGTGCTTTTGCAAAGAAATTATCTGATGCACCTTTAGCTATTGTAGACAAGAGGCGCCATGGACACAATGTTGCTGAGgtaataacggcaacaaaatctgcattgtatccttgaaatgccaaatctttctttttttttcatttatttaacagagtacttttaaacagatt--ttattggg--

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 5
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaa-gtattcttgtactatgttatt--tgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaatatcaacttcatagcttaa-atattagttt
|||||| || ||||| || || ||||| |||||||||||  ||||||||||||||||||| ||||| ||||||||  | || || || ||||| || |||| ||   ||  ||| || |   ||    || || |  |   | |  |      | | ||| | | ||          |  | |  | |||||  | ||      
TGTTGGTGGAGTTGCTAGAGCGCGTGCTTTTGCCAAAAAATTGTCAGATGCACCTCTAGCCATTGTGGATAAAAGGCGCCATGGGCACAATGTTGCAGAGgtaacacatatttgaacaaatctaacaatggtttacaatattggtaaaaagcctagttgtttgttgatttcttcatccttcattttggcttattacatct----

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 5'ss of exon 5
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtactatgttatttgcttaaacagtgt--agccagccaaatggatgtatatagaagaaaaatatcaacttcatagcttaaatattagttt
||||||||| ||||| || |||||||| ||||| || ||| |||| ||||| ||| |||| || || ||||||||  | |||||||||||||| ||||||| || |        |  |       | | | | |  | |  | |   |  | |||||     | |    || ||||  | |  |    ||   | ||   ||
TGTTGGAGGAGTTGCAAGAGCACGTGCTTTTGCAAAGAAGTTGTCTGATGCGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAGgtaatttccacaccaaaactcagcctacattatctttttccaacttactcattggattgccttggtt--aacatattcattataatttttttcttttgtctt

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S42_193V6.3 (Physcomitrella patens), 5'ss of exon 5
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtactatgttatttgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaa-tatcaacttcatagcttaaatattagttt----
|||||| || || ||  | || ||||| ||||| |||||| |||||||||| || ||||||||||| || ||| |||| ||||| ||||| ||  | |||| || |   | |   |  |   |    ||  |       |  ||  ||| ||  ||| |  |    |  |  |||||   |  |     |||| ||    |    
TGTTGGGGGAGTAGCTCGTGCCCGTGCATTTGCTAAAAAGTTGTCAGATGCTCCGCTAGCTATTGTGGACAAACGAAGACAAGGGCATAACGTTTCAGAGgtaaatcaacattagcattaagaccaactcca----ctcaatcatacaa-tgtgtgtgtgcaatttacgacctatcattcttctctgcgaaatgttctgatgcat

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|211009691|gb|FL435043.1|FL435043
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|211126323|gb|FL371824.1|FL371824
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|60338563|gb|DN205536.1|DN205536
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|91052223|gb|EB162641.1|EB162641
EST:     CACCTCTAGTTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|71429936|gb|DR810986.1|DR810986
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGA
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGA
EST: gi|74243299|gb|DT651213.1|DT651213
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|78085035|gb|DV513428.1|DV513428
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|60350838|gb|DN217811.1|DN217811
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|71429935|gb|DR810985.1|DR810985
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|76011084|gb|DT938254.1|DT938254
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|93016209|gb|EB641729.1|EB641729
EST:     AATGTCGCTGAG                         GGGAGGAATTTTATTGGAGACGGGAGAGGAAAAGTGGCTGTTTTGATGGAT
genomic: AATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|86468618|gb|DY234988.1|DY234988
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|78544258|gb|DV621756.1|DV621756
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|110204864|gb|EC886761.1|EC886761
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|60398185|gb|DN231001.1|DN231001
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|78125653|gb|DV544037.1|DV544037
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
EST: gi|26457160|gb|CA828743.1|CA828743
EST:     CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAG                         GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT
genomic: CACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattc ... tttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGAGGTGTTGCCAGGGCACGTGCCTTTGCCAAAAAGCTGTCAGATGCACCTCTAGCTATTGTAGATAAAAGAAGGCAAGGACATAATGTCGCTGAGgcaagtattcttgtactatgttatttgcttaaacagtgtagccagccaaatggatgtatatagaagaaaaatatcaacttcatagcttaaatattagttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG