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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGTGGCTCTGGCGGGGGTGGAGAGGCGGCGGCCGGAGGCGGCGTCGCTCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttacagtccctgtgcgtggctcgtgagcagcggcagcgcatcgtgcttgtagattttttcttggatggtgctgcatgtatagagttgttaagga...

Basic information

species Zea mays
transcript GRMZM2G002440_T02
intron # 1
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|91873086|gb|EB403043.1|EB403043
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211486479|gb|FL110811.1|FL110811
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211483602|gb|FL110803.1|FL110803
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211159401|gb|FL365678.1|FL365678
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211486475|gb|FL110807.1|FL110807
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211519817|gb|FL338576.1|FL338576
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211543369|gb|FL321070.1|FL321070
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTACGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211356792|gb|FL332225.1|FL332225
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211309955|gb|FL324302.1|FL324302
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211483605|gb|FL110806.1|FL110806
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211483601|gb|FL110802.1|FL110802
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211365235|gb|FL351459.1|FL351459
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTTYA
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTC-A
EST: gi|50332491|gb|CO527617.1|CO527617
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211486478|gb|FL110810.1|FL110810
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211010679|gb|FL358969.1|FL358969
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211037801|gb|FL314005.1|FL314005
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211086851|gb|FL356798.1|FL356798
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCATG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211536909|gb|FL308322.1|FL308322
EST:     TCATGGGGGCGCCTGTGCTTGCTACTGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|101400819|gb|EB822107.1|EB822107
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211486477|gb|FL110809.1|FL110809
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211486476|gb|FL110808.1|FL110808
EST:     TCATGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
EST: gi|211483603|gb|FL110804.1|FL110804
EST:     TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAG                         GTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG
genomic: TCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 124

CTCTGTGGCTCTGGCGGGGGTGGAGAGGCGGCGGCCGGAGGCGGCGTCGCTCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAGAGGTTTGGGTTTTCAACTTCAGCCCCCCAACAAGATGATAAGGAGACAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 67

CTCTGTGGCTCTGGCGGGGGTGGAGAGGCGGCGGCCGGAGGCGGCGTCGCTCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAGAGGTTTGGGTTTTCAACTTCAGCCCCCCAACAAGATGATAAGGAGACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

CTCTGTGGCTCTGGCGGGGGTGGAGAGGCGGCGGCCGGAGGCGGCGTCGCTCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAGAGGTTTGGGTTTTCAACTTCAGCCCCCCAACAAGATGATAAGGAGACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

CTCTGTGGCTCTGGCGGGGGTGGAGAGGCGGCGGCCGGAGGCGGCGTCGCTCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttac ... ttacaagcagGTCATTCCTTTGTCGAATCAGCTGGCTCGATACTCGACAACTGCATTTCAGAGGTTTGGGTTTTCAACTTCAGCCCCCCAACAAGATGATAAGGAGACAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGTGGCTCTGGCGGGGGTGGAGAGGCGGCGGCCGGAGGCGGCGTCGCTCCTGGGGGCGCCTGTGCTGGCTACGGTGGAAGCCTGCGCTTCGATCAAGgtggtgttacagtccctgtgcgtggctcgtgagcagcggcagcgcatcgtgcttgtagattttttcttggatggtgctgcatgtatagagttgttaagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG