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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCATGGCGACCGCGCTCAAGTCGTTCTTGAACAGCCCCGTTGGCCCCAAGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctctgcagttcatgcttgggttcttacgcttacgcaaatctgtgcgattcgcggacttcaacaacgcacgcaacgtaatttttgcaattatatt...

Basic information

species Zea mays
transcript GRMZM2G139805_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139805_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g31830.1 (Oryza sativa), 5'ss of exon 2
CCTCATGGCGACCGCGCTCAAGTCGTTCTTGAACAGCCCCGTTGGCCCCAAGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctctgcagttcatgcttgggttcttacgcttacgcaaatctgtgcgattcgcggacttcaacaacgcacgcaacgtaatttttgcaattatatt-------
   ||||||||| |||   ||| |||||| |||||||||||| ||||||| |||||||||||||||||| || || || ||||||||||||||| ||||||||||    | |  | |   ||     |  |  |   | |  | | ||  ||||| | |  ||   |    |     | | || |||   ||| || |         
GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacatac--taccgtctaataataatcggtcaatgtcattttg--cgatttgggtgctgtgattttg---atatcatattttggtcaagtagaacgtggcgc
















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|211091208|gb|FK989718.1|FK989718
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211088760|gb|FK989708.1|FK989708
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCNAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211088757|gb|FK989705.1|FK989705
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|86465672|gb|DY232045.1|DY232045
EST:     AGACCACCCACTTCGGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAACCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211088761|gb|FK989709.1|FK989709
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091214|gb|FK989724.1|FK989724
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091201|gb|FK989711.1|FK989711
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091211|gb|FK989721.1|FK989721
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|86465671|gb|DY232044.1|DY232044
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211088759|gb|FK989707.1|FK989707
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091207|gb|FK989717.1|FK989717
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091202|gb|FK989712.1|FK989712
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091209|gb|FK989719.1|FK989719
EST:     MGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091213|gb|FK989723.1|FK989723
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211394695|gb|FL474336.1|FL474336
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091212|gb|FK989722.1|FK989722
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211088762|gb|FK989710.1|FK989710
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091204|gb|FK989714.1|FK989714
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091203|gb|FK989713.1|FK989713
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091206|gb|FK989716.1|FK989716
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
EST: gi|211091205|gb|FK989715.1|FK989715
EST:     AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCG                         GGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACA

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: 51

CCTCATGGCGACCGCGCTCAAGTCGTTCTTGAACAGCCCCGTTGGCCCCAAGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 35

CCTCATGGCGACCGCGCTCAAGTCGTTCTTGAACAGCCCCGTTGGCCCCAAGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACAGCAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 34

CCTCATGGCGACCGCGCTCAAGTCGTTCTTGAACAGCCCCGTTGGCCCCAAGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACAGCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 45

CCTCATGGCGACCGCGCTCAAGTCGTTCTTGAACAGCCCCGTTGGCCCCAAGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctct ... ttttttgcagGGCTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAACATGACAGCAG