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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgctagtgggattttttttctggactgatgatgcaacggtgcctgaacctcttgcgcgtgtctctggttgaagtttttattggtgggtttccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 1
ctgctagtgggattttttttctggactg-----atgat-gcaacggtgcctgaacc-tcttgcgcgtgtctctggttgaagtttttattggtgggtttccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT
       |    |||| |||  ||  ||     ||||| |||  ||||||| |||| || |  | | |     || |||| || || || ||  |||||  || |||||||||||||| || |||||||| |||||| ||| ||  ||||| || ||||| |||||||| 
-----gatttttttttatttggggggtgttgcgatgattgcattggtgcctaaaccctcgtttgtgcgggcacggatgaatttgtt-ttcgtttgtttctctg-tagGAACAAGCGCGTGGTAAGGCTGGAGGGCAGCCCAGCTATGGCGGCGGCGCGTTCTACATGCCG
















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|76929603|gb|DV172080.1|DV172080
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|88755248|gb|DY539389.1|DY539389
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211170206|gb|FL095741.1|FL095741
EST:     GRCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: G-CGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211171878|gb|FL095747.1|FL095747
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGATGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|22819595|gb|BU499685.1|BU499685
EST:     GACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGAGCGGAGG-GC
genomic: GACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCG-GCGGTGGTGC
EST: gi|211170205|gb|FL095740.1|FL095740
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|28566548|gb|CB278196.1|CB278196
EST:     GCGCTACGACGGCAACCCCTTCGAGCGAGGATGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GCGCTACGACGGCAACCCCTTCGAG-GAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211171877|gb|FL095746.1|FL095746
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGATGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211170209|gb|FL095744.1|FL095744
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|42491841|gb|CK700887.1|CK700887
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGATGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|37622034|gb|CF675087.1|CF675087
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGATGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211170207|gb|FL095742.1|FL095742
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211170208|gb|FL095743.1|FL095743
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211170204|gb|FL095739.1|FL095739
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGTCTGGCGGGCAGTCCAACTTCGGCGGTGGTGC
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGG-CTGGCGGGCAGTCCAACTTCGGCGGTGGTGC
EST: gi|38568932|gb|CF974817.1|CF974817
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGATGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|211171876|gb|FL095745.1|FL095745
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     GGCGCTACGACGGCAACCCCTTCGAGGAGGATGACGTGAACCCTTTCTCG                         GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG
genomic: GGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCG

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: 128

CTCTGTTCGGCAGGACTCCTTCAAGCAGAAGGGGCGGAGCAGCATGGCGGGGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

CTCTGTTCGGCAGGACTCCTTCAAGCAGAAGGGGCGGAGCAGCATGGCGGGGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

CTCTGTTCGGCAGGACTCCTTCAAGCAGAAGGGGCGGAGCAGCATGGCGGGGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

CTCTGTTCGGCAGGACTCCTTCAAGCAGAAGGGGCGGAGCAGCATGGCGGGGCGCTACGACGGCAACCCCTTCGAGGAGGAGGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacctcttgcgcgtgtctctggttgaagtttttattggtgggtttccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT
                                           tttcctt  CT-rich tract
                       ttgaagtttttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgctagtgggattttttttctggactgatgatgcaacggtgcctgaacctcttgcgcgtgtctctggttgaagtttttattggtgggtttccttgatagGAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT

ctgctag
- - - - - - - - ttttctg
- - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - -gcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggg