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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC

Basic information

species Zea mays
transcript GRMZM2G179308_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
-----------------acctacccaagattt--acctt------gccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
                 |||||    |  |||   ||||      | | | |  ||      ||  | || | ||   | |   | | |    |||  | || |||||  |    || | ||||||||||||||||| || |||||||| || ||||||| ||||| | |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| || |
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC

upper sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 6
acctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttag---tgaatattgaata--tggtactgatcctc--tttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
         | | | |     ||  |||  ||   ||| || |  || ||||| ||      | ||   ||   ||  |   ||      || |||  ||||   ||  | || || |||| ||||      | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |       
------aggaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgagatcactgacatccattgctgattgtttatatttaacagAGTACAACCAGATCACCAA------GTTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
acctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagt----gaatattgaata-tggtactgat--cctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
        || | | |     ||  |||  ||   ||| || |  || ||||| ||     |||   |||  | ||  |   ||  | | || |||  ||||   ||  | || || |||| ||||      | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |       
------ggaaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
acctacccaagatttaccttgccctgtgct-tgttgatttctgttgtaataggttagtgaa-tattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
            | || || |       || |||       |  |||       || | || |  ||||   || | |  |  |  | ||| |   |||  ||     |||||||  | || ||| | || ||||   ||  | ||||| || || ||||| || ||||||||||||||||||||||| || ||||| |  |      
-----------gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaa---ggaatt--tggttgtgtttcctgatgcagGG----GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC

upper sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------acctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttag---tgaatattgaatatggtactgatcct----ctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
                                                         |||     |||||    |     |   |  || |  | |     |||     |  ||||    |||  | ||| || |     || |||  | |||| ||||| |  | || || ||||| || |||   | ||| |||  | |||| |  || |||||||| |||||||||||||||||||||||  | | |||    |
gtatatctacttctgttctggtagcttttcaatttgtttgcacttctgttgttctttcaatcaagaccttattgttgatattcaggcttttccttttccctgttccctttccatatcagttattat-ctggtcataatgtttctttctaattgc-agGTTACCACACGGTCACCAAAAGATGGAATATGTTATAAGAAGTTGCCAAGATCAAGTGCTATTAAGGTGATTGATTTTGGTAGCACAGCTTTTGAGTGTC

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|211248594|gb|FL451517.1|FL451517
EST:     GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAG                         GTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAGgtgagtttgc ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
EST: gi|32850031|gb|CD989712.1|CD989712
EST:     GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAG                         GTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAGgtgagtttgc ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
EST: gi|32934327|gb|CF039139.1|CF039139
EST:     GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAG                         GTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGATGAAAGTAGATCTAGgtgagtttgc ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
                           tactgat  putative branch site (score: 2)
                                 tcctctttttttcatt  CT-rich tract
           tgaatattgaatat  TA-rich tract