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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttgtttcctctcctgtgcgagctacatatgacttggttatttgttaacctttatttcctgtaaaattgcttttgtttctttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT

Basic information

species Zea mays
transcript GRMZM5G812553_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G812553_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 6
gtatatttgtttcctctcctgtgcgagctacatatgacttggttatttgttaacctttatttcctgtaaaattgcttttgtttctttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT-------
||||||||       |||| |    | |||||||||   |     || | |||||| || || |  | |  || ||||  |||  |   ||||||||||||||||| ||||| |||||||||||||||       
gtatattt-------ctccagcataatctacatatggtgt-----ttagataacctctactttcactgatgtttctttc-ttttgtgcaaccagGACAAATGATCCTCATGAGGCGATTGATCGAATTGTGAGAG
















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|78105462|gb|DV523880.1|DV523880
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|149080870|gb|EE169951.2|EE169951
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|40334416|gb|CK368486.1|CK368486
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|91878207|gb|EB408164.1|EB408164
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTG
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATTG
EST: gi|31363680|gb|CD448037.1|CD448037
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCTATTGATCGAATTG
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATTG
EST: gi|76285904|gb|DV025472.1|DV025472
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|211469689|gb|FK976086.1|FK976086
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|71298751|gb|DR785364.1|DR785364
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|93281461|gb|EB673725.1|EB673725
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|91051589|gb|EB162007.1|EB162007
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|32867365|gb|CF007047.1|CF007047
EST:     CTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTGT
genomic: CTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAA-T-T
EST: gi|30087080|gb|CB885288.1|CB885288
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTG
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATTG
EST: gi|8102673|gb|AW927320.1|AW927320
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTGT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAA-T-T
EST: gi|50336722|gb|CO531848.1|CO531848
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|78113487|gb|DV531878.1|DV531878
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|71436209|gb|DR817259.1|DR817259
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|50322460|gb|CO517586.1|CO517586
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|76021472|gb|DT948642.1|DT948642
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|50334433|gb|CO529559.1|CO529559
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTGT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAA-T-T
EST: gi|148976019|gb|EE025878.2|EE025878
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCC-ATGACGCGATTGATCGAATT
EST: gi|33467744|gb|CF244793.1|CF244793
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTG
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGG-CTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATTG
EST: gi|78078210|gb|DV506625.1|DV506625
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|78121934|gb|DV540318.1|DV540318
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTGT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAA-T-T
EST: gi|78075654|gb|DV504088.1|DV504088
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|27522138|gb|CA989244.1|CA989244
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTG
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATTG
EST: gi|71764065|gb|DR962002.1|DR962002
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|78085115|gb|DV513508.1|DV513508
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCC-ATGACGCGATTGATCGAATT
EST: gi|89759547|gb|DY688342.1|DY688342
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|30307231|gb|CD001904.1|CD001904
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|78121935|gb|DV540319.1|DV540319
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|40335239|gb|CK369309.1|CK369309
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|71774560|gb|DR972438.1|DR972438
EST:     CTCTTTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|71436272|gb|DR817322.1|DR817322
EST:     CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATT
genomic: CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
EST: gi|78105461|gb|DV523879.1|DV523879
EST:     CAGATTTTGCTCGGACATTTGGCTG                         GACAAATGATCCCCATGACGCGATTGATCGAATTGT
genomic: CAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAA-T-T

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: 47 (upstream exon), 49 (downstream exon)
Score: 121

CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 130

CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 76

CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 121

CTCATTCCACTTGGAACTGGCTCAGATTTTGCTCGGACATTTGGCTGgtatatttgt ... tttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttatttgttaacctttatttcctgtaaaattgcttttgtttctttttaccagGACAAATGATCCCCATGACGCGATTGATCGAATT
        tgttaac  putative branch site (score: 121)
                                ttgcttttgtttcttt  putative PPT
                                    ttttgtttcttttta  TA-rich tract