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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaaatgtgcattgccttctcacgtgcaaaatgcagctgtaatgtacacacttactagaaaatgctgttcagcgctaccaataacatgtgctttatccag

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 3
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|76929603|gb|DV172080.1|DV172080
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|88755248|gb|DY539389.1|DY539389
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|26559874|gb|CA832109.1|CA832109
EST:     AACCAGCAGACTTCAGTGCTACAGAGGACATACCCCGGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211171878|gb|FL095747.1|FL095747
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     GGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: GGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|22819595|gb|BU499685.1|BU499685
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|37621887|gb|CF674940.1|CF674940
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211170205|gb|FL095740.1|FL095740
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|28566548|gb|CB278196.1|CB278196
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTACAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211171877|gb|FL095746.1|FL095746
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211170209|gb|FL095744.1|FL095744
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|42491841|gb|CK700887.1|CK700887
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|37622034|gb|CF675087.1|CF675087
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211170207|gb|FL095742.1|FL095742
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211170208|gb|FL095743.1|FL095743
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAASCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211170204|gb|FL095739.1|FL095739
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCTAGCAAGGGAACGCGGAATTGAA
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAA-GCGGAATTGAA
EST: gi|38568932|gb|CF974817.1|CF974817
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|211171876|gb|FL095745.1|FL095745
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAG                         GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC
genomic: AACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAAC

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: 251

CAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 230

CAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

CAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 478

CAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaa ... ctttatccagGACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGTCAAAGgtgcgagtaaatgtgcattgccttctcacgtgcaaaatgcagctgtaatgtacacacttactagaaaatgctgttcagcgctaccaataacatgtgctttatccag

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