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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGAGAGGTGGATTCGGCAGCAGGAGGTGAGGACCTGGAGCCGCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattgcgttgctcttcgtggacttgagttgagtaccttaggatttgctggtttcgatgtgcag

Basic information

species Zea mays
transcript GRMZM2G073404_T02
intron # 2
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|22521374|gb|BU080185.1|BU080185
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|113701973|gb|EE679477.1|EE679477
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370522|gb|FL006750.1|FL006750
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|93281783|gb|EB674047.1|EB674047
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370518|gb|FL006746.1|FL006746
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370526|gb|FL006754.1|FL006754
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370515|gb|FL006743.1|FL006743
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370517|gb|FL006745.1|FL006745
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|26456679|gb|CA828262.1|CA828262
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211373170|gb|FL006758.1|FL006758
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|20507614|gb|BQ279704.1|BQ279704
EST:     GCTCTTCGACTACATTCTAGTGCATCCTAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211373167|gb|FL006755.1|FL006755
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|22549117|gb|BU101318.1|BU101318
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370525|gb|FL006753.1|FL006753
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211373173|gb|FL006761.1|FL006761
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370523|gb|FL006751.1|FL006751
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370516|gb|FL006744.1|FL006744
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211373171|gb|FL006759.1|FL006759
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370521|gb|FL006749.1|FL006749
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|67013821|gb|CO442570.1|CO442570
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370524|gb|FL006752.1|FL006752
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370514|gb|FL006742.1|FL006742
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211373169|gb|FL006757.1|FL006757
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|50322317|gb|CO517443.1|CO517443
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|67015419|gb|CO444168.1|CO444168
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211370519|gb|FL006747.1|FL006747
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
EST: gi|211373174|gb|FL006762.1|FL006762
EST:     GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACG                         ACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA
genomic: GCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 139

GCAGGAGAGGTGGATTCGGCAGCAGGAGGTGAGGACCTGGAGCCGCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAAAGGTCCACACCTCCACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 222

GCAGGAGAGGTGGATTCGGCAGCAGGAGGTGAGGACCTGGAGCCGCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAAAGGTCCACACCTCCACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

GCAGGAGAGGTGGATTCGGCAGCAGGAGGTGAGGACCTGGAGCCGCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAAAGGTCCACACCTCCACG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 123

GCAGGAGAGGTGGATTCGGCAGCAGGAGGTGAGGACCTGGAGCCGCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattg ... cgatgtgcagACAGCGACTTGGAGGTGGCCGACATCTTCAAATACTGCAACAAGCGCCCAAAGGTCCACACCTCCACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGAGAGGTGGATTCGGCAGCAGGAGGTGAGGACCTGGAGCCGCTCTTCGACTACAAGCGAGTGCAGCCCAGGATGACGTTCTGCTTTGACGgtacgcattgcgttgctcttcgtggacttgagttgagtaccttaggatttgctggtttcgatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG