Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctaatttctagtaacctccaccattttattattttattgcttttctcattcaatatttctttgttttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA

Basic information

species Zea mays
transcript GRMZM2G180704_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 9
-----gtaatctaatttctagtaacctccaccatt-------ttattattttattgcttttctcat---tcaatatttctt------tgttttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA
     |   | | | || | ||||      ||||        || |  ||||  ||  ||  |  |   |  ||| || ||      | | |||||  |||||||||| |||||    ||||||||| |||| || || |||||| ||||||||||||||||||  ||||| ||||| |||||||| ||||||||||| |
taacggctgtttgaatttttgtaatagttgccatcagaaaaattgtagttttgatgtcttgttggtagttatatactttttgttcattatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 10
----------gtaatctaatttc-tagtaacctccaccatt----ttattattttattgcttttct------cattcaatatttctttgttttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA
          |   | |  |||  || ||    ||| ||      || |  | ||  ||  ||  |       | | | | ||| ||| | |||||  |||||||||| |||||    ||||||||| |||| || || |||||| ||||||||||||||||||  ||||| ||||| |||||||| ||||||||||| |
atatctaaaagctgtttgtttttgtaatagtggccatcagaaaaattgtagtcttgatgtcttgttggtagttacttactttttgtttatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTTCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
------------------gtaatctaatttctagtaacctccaccattttattatttt--attgcttttctcattcaatatttct-ttgttttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA
                     ||  || ||||  |   ||        |  ||| ||   | ||   |  |  ||   ||| | | ||   ||||| ||||||||||| || |||   ||||||||| |||| || || |||||||| ||||||||||||||||  ||||| ||||| || |||||||||||||||||||
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
---gtaatctaatttctagtaacc-tccaccattttattattttattgcttttctcattcaatatttctttgttttgtgt---tagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA
    | || |  | | || | |   |  |     ||    ||||  |   | | | ||| ||||||       ||||       ||||||| || |||||    ||||||||| | ||||| |||||||| |||||||| || ||||| |  ||||| |||||||| ||||| |||||||||||||
gttttgatattttctgtatttatggtataaagacttcagcttttgatatatatgtgatt-aatattgtaacaatttgatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA

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|148974738|gb|EE025549.2|EE025549
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|5871525|gb|AW017996.1|AW017996
EST:     CAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCNCATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: CAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|60348073|gb|DN215046.1|DN215046
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|6095545|gb|AW120212.1|AW120212
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|211339633|gb|FL428844.1|FL428844
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|67022796|gb|CO451545.1|CO451545
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGNCA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTG-CA
EST: gi|94477170|gb|EB706128.1|EB706128
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|6031408|gb|AW076310.1|AW076310
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|6994173|gb|AW453387.1|AW453387
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|60401527|gb|DN234334.1|DN234334
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|60339141|gb|DN206114.1|DN206114
EST:     AGGAAATGGGCTCTTGGTCTTCAG                         TCTTGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: AGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|116827763|gb|EC871704.1|EC871704
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|76015667|gb|DT942837.1|DT942837
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|60400026|gb|DN232833.1|DN232833
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|211092258|gb|FL379383.1|FL379383
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|76015666|gb|DT942836.1|DT942836
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|32847442|gb|CD987123.1|CD987123
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|149088706|gb|EE177827.2|EE177827
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|78022885|gb|DV491272.1|DV491272
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
EST: gi|94473980|gb|EB702938.1|EB702938
EST:     GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAG                         TCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA
genomic: GCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 189

AAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

AAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

AAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

AAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCACATCTTCCAGCTGAGAGGAAATGGGCTCTTGGTCTTCAGgtaatctaat ... tttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattttattattttattgcttttctcattcaatatttctttgttttgtgttagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA
                                  tatttctttgtttt  CT-rich tract
     tttattattttattgc  TA-rich tract