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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCGTCGCCCCCGCCAAAACCTTCATCTGCCGGGGCTGCACCGGCGGCGCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaaccctacgttccacgggttcgtttcatgcagcgagatctctcatttctctgctgcggctgcgggtttcggttcgtaatcttactgtctgcgt...

Basic information

species Zea mays
transcript GRMZM2G044348_T04
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|149012865|gb|EE042709.2|EE042709
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|71435689|gb|DR816739.1|DR816739
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|148948442|gb|EC893960.2|EC893960
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|211267468|gb|FK986910.1|FK986910
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|149027788|gb|EE286084.2|EE286084
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|148991460|gb|EE032969.2|EE032969
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCCACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|148948218|gb|EC893734.2|EC893734
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32921110|gb|CF025922.1|CF025922
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|91875915|gb|EB405872.1|EB405872
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32920943|gb|CF025755.1|CF025755
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|149097124|gb|EE182936.2|EE182936
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|50330013|gb|CO525139.1|CO525139
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|17930295|gb|BM267255.1|BM267255
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32808001|gb|CD960235.1|CD960235
EST:     GATCTGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|149001048|gb|EE038297.2|EE038297
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32797849|gb|CD950085.1|CD950085
EST:     GATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|149100817|gb|EE186911.2|EE186911
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|78088713|gb|DV517106.1|DV517106
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|17930284|gb|BM267244.1|BM267244
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|149110465|gb|EE190430.2|EE190430
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|149067509|gb|EE157716.2|EE157716
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|148976595|gb|EE025942.2|EE025942
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32920656|gb|CF025468.1|CF025468
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32921020|gb|CF025832.1|CF025832
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|31360319|gb|CD444676.1|CD444676
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGGGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32920553|gb|CF025365.1|CF025365
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32803016|gb|CD955252.1|CD955252
EST:     GATCCCGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32920675|gb|CF025487.1|CF025487
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|148943973|gb|EC889054.2|EC889054
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|211267467|gb|FK986909.1|FK986909
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|148930101|gb|EC872413.2|EC872413
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|94475590|gb|EB704548.1|EB704548
EST:     GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
EST: gi|32797933|gb|CD950169.1|CD950169
EST:     GATCCTGTGACTGATCTCTTCGTTCCTCG                         GTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT
genomic: GATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGT

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), 49 (downstream exon)
Score: 311

TCTTCGTCGCCCCCGCCAAAACCTTCATCTGCCGGGGCTGCACCGGCGGCGCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGTTCCTAACAATGAGGGCACATGAACGAGCTGCCAGTTTGGCTCTTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 440

TCTTCGTCGCCCCCGCCAAAACCTTCATCTGCCGGGGCTGCACCGGCGGCGCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGTTCCTAACAATGAGGGCACATGAACGAGCTGCCAGTTTGGCTCTTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 372

TCTTCGTCGCCCCCGCCAAAACCTTCATCTGCCGGGGCTGCACCGGCGGCGCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGTTCCTAACAATGAGGGCACATGAACGAGCTGCCAGTTTGGCTCTTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 405

TCTTCGTCGCCCCCGCCAAAACCTTCATCTGCCGGGGCTGCACCGGCGGCGCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaac ... atcttcgcagGTTCACTTTGATATTCCAACAAAGGTCACATTGCTAGACTCCCAGATTGGTTCCTAACAATGAGGGCACATGAACGAGCTGCCAGTTTGGCTCTTGCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCGTCGCCCCCGCCAAAACCTTCATCTGCCGGGGCTGCACCGGCGGCGCGGGGACAACAAAAGCTCGAGATCCGGTGACTGATCTCTTCGTTCCTCGgtgagtaaaccctacgttccacgggttcgtttcatgcagcgagatctctcatttctctgctgcggctgcgggtttcggttcgtaatcttactgtctgcgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC