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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagttcttttttatcacatagctatatcgtttgacatgcctaactccatgattctcctttgatggctgatgctgaacatttgacgcatacacag

Basic information

species Zea mays
transcript GRMZM2G153087_T01
intron # 4
splice site 5'
intron type U2

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|211327259|gb|FL468829.1|FL468829
EST:     AAGAAAAAACTCCTAAAAGCAACAGTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCAAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|76292992|gb|DV032560.1|DV032560
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|76282003|gb|DV021571.1|DV021571
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATTTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|71326250|gb|DR799818.1|DR799818
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCANAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|76282004|gb|DV021572.1|DV021572
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGGATGCCACCTCC
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAG-ATGCCACCTCC
EST: gi|71772104|gb|DR970041.1|DR970041
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|149014987|gb|EE044728.2|EE044728
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|78090616|gb|DV518990.1|DV518990
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|78075129|gb|DV503563.1|DV503563
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|32800843|gb|CD953079.1|CD953079
EST:     TAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATACGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: TAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|113703593|gb|EE681097.1|EE681097
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|29543426|gb|CB603822.1|CB603822
EST:     CTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: CTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|211268203|gb|FL248419.1|FL248419
EST:     AGAAAAAACTCCTAAAAGCAACAGTAAGACTAANCAA-TCTGGCTCAAAG                         CCCTCGCGCCATGCGGAA
genomic: AGAAAAAACTCCTAAAAGCAACATTAAGACTAA-CAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAA
EST: gi|76013927|gb|DT941097.1|DT941097
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|31357900|gb|CD442257.1|CD442257
EST:     AAGAAAAAACTCCTAAAAGCAACAGTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCAAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|71311485|gb|DR792097.1|DR792097
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|76292991|gb|DV032559.1|DV032559
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATTTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|71326247|gb|DR799817.1|DR799817
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|78090615|gb|DV518989.1|DV518989
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|211301905|gb|FL443567.1|FL443567
EST:     AAGAAAAAACTCCTAAAAGCAACAGTAAGACTAACAAATCTGGCTCAAAG                         CCCTCGCGCCATGCGGAACCAAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
EST: gi|71311486|gb|DR792098.1|DR792098
EST:     AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCANAG                         CCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA

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: 33 (upstream exon), 49 (downstream exon)
Score: 111

CCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGAGGAGGAAGGGGAACCACAGGAAGACCAGG


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 113

CCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGAGGAGGAAGGGGAACCACAGGAAGACCAGG


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 103

CCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGAGGAGGAAGGGGAACCACAGGAAGACCAGG


Block sizes: 33 (upstream exon), 42 (downstream exon)
Score: 37

CCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gcatacacagCCCTCGCGCCATGCGGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGAGGAGGAAGGGGAACCACAGGAAGACCAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAACATTAAGACTAACAAATCTGGCTCAAAGgtatatagttcttttttatcacatagctatatcgtttgacatgcctaactccatgattctcctttgatggctgatgctgaacatttgacgcatacacag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA