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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgaccgccccacggtcaggctctaaagtctgaaccctaagccctggccgcggccgacgcgagtgactgtgcttccccttgtgttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGCGGACGCTTCCGCGGCGGCCTCGGAGCTAGATGGGCTGCCGCGCTTCGAG

Basic information

species Zea mays
transcript GRMZM2G143246_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g10050.2 (Oryza sativa), 3'ss of exon 1
gtaattgaccgccccacggtca-ggctctaaagtctgaaccctaagccctggccgcggccgacgc-gagtgactgt--gcttccccttgtgttccatc-cagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGCGGACGCTTCCGCGGCGGCCTCGGAGCTAGATGGGCTGCCGCGCTTCGAG
     | ||||| ||||   |  || | | |  ||| |||||||||||||    |  |  |   | || ||   ||  | ||    | | |||   |  |||||| ||||||||||| |||||| ||||||||||| |  || |||||||||||||| |  | || |||||| | || || |||||||||||||| ||||||
----gtaaccgctccaccaccgtggttttgatttctaaaccctaagccctaagtgttgggggttctgattgctcgttgggttgggttggggtttggttgcagCGAAGGGGCGTTCGGGGGCGGGACGAGGGCGTTCGCCCCGACGAGCAAGGCGGACTCCGCGGCCGCGGCCGCTGACCTGGATGGGCTGCCGCGGTTCGAG
















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|211108445|gb|FL061185.1|FL061185
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|71774216|gb|DR972094.1|DR972094
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|148990097|gb|EE031861.2|EE031861
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211107537|gb|FL061178.1|FL061178
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|78081135|gb|DV509547.1|DV509547
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211107538|gb|FL061179.1|FL061179
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211107541|gb|FL061182.1|FL061182
EST:     CGCTACGACGG-CGCGCTGCGGACGCGGGCTCCTACCGCGACCG-CGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|149099803|gb|EE185855.2|EE185855
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211107542|gb|FL061183.1|FL061183
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|76287087|gb|DV026655.1|DV026655
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|86472666|gb|DY239036.1|DY239036
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|94477391|gb|EB706349.1|EB706349
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|93017517|gb|EB643037.1|EB643037
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|91053059|gb|EB163477.1|EB163477
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211107539|gb|FL061180.1|FL061180
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|78074504|gb|DV502938.1|DV502938
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211108455|gb|FL061195.1|FL061195
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|78077833|gb|DV506262.1|DV506262
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|78120999|gb|DV539383.1|DV539383
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAGGGG
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211108449|gb|FL061189.1|FL061189
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|211108453|gb|FL061193.1|FL061193
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|148938225|gb|EC882515.2|EC882515
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|149105515|gb|EE291040.2|EE291040
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|148952300|gb|EC898110.2|EC898110
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|149005479|gb|EE040035.2|EE040035
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|148931912|gb|EC875118.2|EC875118
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|78083647|gb|DV512040.1|DV512040
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC
EST: gi|88751705|gb|DY535846.1|DY535846
EST:     CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAG                         CGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAGGGG
genomic: CGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGC

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 3 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 12

CGCCTAAACCCTAGCCATCCTCCTCGCCGCCGGCGACCGCCGCCATGAGCCGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGCGGACGCTTCCGCGGCGGCCTCGGAGCTAGATGGGCTGCCGCGCTTCGAG


Block sizes: 36 (upstream exon), 14 (downstream exon)
Score: 1

CGCCTAAACCCTAGCCATCCTCCTCGCCGCCGGCGACCGCCGCCATGAGCCGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGCGGACGCTTCCGCGGCGGCCTCGGAGCTAGATGGGCTGCCGCGCTTCGAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 3

CGCCTAAACCCTAGCCATCCTCCTCGCCGCCGGCGACCGCCGCCATGAGCCGCTACGACGGCCGCGCTGCGGACGCGGGCTCCTACCGCGACCGCCGCAGgtaattgacc ... ttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGCGGACGCTTCCGCGGCGGCCTCGGAGCTAGATGGGCTGCCGCGCTTCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagccctggccgcggccgacgcgagtgactgtgcttccccttgtgttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGCGGACGCTTCCGCGGCGGCCTCGGAGCTAGATGGGCTGCCGCGCTTCGAG
                                 cttccccttgtgttcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgaccgccccacggtcaggctctaaagtctgaaccctaagccctggccgcggccgacgcgagtgactgtgcttccccttgtgttccatccagCGAGGGGGCGTTCGGAGGCGGGTCGAGGGCGTTCTCGGCGCCGAGCAAGGCGGACGCTTCCGCGGCGGCCTCGGAGCTAGATGGGCTGCCGCGCTTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT