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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttaaattgggtgtattcacgttcttgcactgcttattttgataaaatcctaagagcttgctgaagacgatacgtgctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG

Basic information

species Zea mays
transcript GRMZM2G165535_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g58580.2 (Oryza sativa), 3'ss of exon 5
gtaagcttaaattgggtgtattcacgttcttgcactgcttattttgata-aaatcctaagagcttgctgaagacgatacgtgctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
            || |  | ||   ||| | |   ||||| ||   | | ||||  ||||  | |||    || ||||| || ||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||| |||||
-----------gtgagccttttttagttatagtgttgcttgttcacacataaattttaaggccatgcaatcgatgatacatgttctttgcagGAATTTATTAACTTCACGCTTCATTACATTGCTGACTTGGACATCCCAATCAAAAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 6
---------gtaagcttaaattgggt-gtattcacgttcttgcactgctt-attttgataaaatcctaagagcttgctgaagacgatac--gtgctctttc-cagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
         || |  || |||    | ||   ||  |           || || |  ||||| ||||      ||  | | |||   |    || | || | ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| ||||| ||
taactacttgtgaaattcaataaaattgtgggcatataaagaaggcattttatatcaataaattcct-----tttaataatgacagaattgatgatgttccgcagGAGTTTATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 6
----------gtaagcttaaattgggt-gtattcacgttcttgcactgctt-attttgataaaatcctaagagcttgctgaagacgatac--gtgctctttc-cagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
          || |  || |||   || ||   ||  |           || || |  ||||| |||     | ||  | | |||   |    || | |    ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| ||||| | 
ttaactacttgtgaaattcaataaagttgtgagcatataaagaaggcattttatatcaataaactcc-----gtttaataatgacagaattgatgatatcctgcaGGAGTTTATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA-

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 5
-gtaagcttaaattgggtgtattcacgttct-tgcactgcttat--tttgataaaatcctaagagcttgctgaagacgatacgtgct------ctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
 ||   |  | ||  | || |  |||   |  |||| |||  ||  ||    | |   ||      ||  ||     |||  ||          | | |||||| ||||||| ||||| |||||||| ||||||||||||||||||||||| |||||
agttctccaacatctgttg-acacacacacaatgcattgcaaatggttgtgcagacgtctgttcatttattgtttttgatgtgttacaaatgattgtgcagGAAATTATTAATTTCACACTTCATTATATTGCTGACTTGGATATCCCAATAAAAAG

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|6020771|gb|AW065579.1|AW065579
EST:     TGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTAANTTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAA
genomic: TGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTT-A-TTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTATATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71449147|gb|DR830197.1|DR830197
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     TTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: TTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|74245816|gb|DT653730.1|DT653730
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71299719|gb|DR785870.1|DR785870
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|32919710|gb|CF024522.1|CF024522
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTATATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|14646044|gb|BI180233.1|BI180233
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71773498|gb|DR971398.1|DR971398
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     AGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     AAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     CCAAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: CCAAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttattttgataaaatcctaagagcttgctgaagacgatacgtgctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
     ttttgat  putative branch site (score: 4)
                                           tgctctttcc  putative PPT
     ttttgataaaat  TA-rich tract