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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACAAATACGCTTTGTTGCCTATTATGAGATCGTACATTGATCATGCCGCAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtctgctgcattgtttattgtaaacagtatacgttcaaggttgtaggcagttcttgatttctaaattatcttaacactttggcag

Basic information

species Zea mays
transcript GRMZM2G032423_T03
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|67029465|gb|CO458214.1|CO458214
EST:     CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAG                         AATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
genomic: CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
EST: gi|91049336|gb|EB159754.1|EB159754
EST:     CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAG                         AATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
genomic: CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
EST: gi|211099307|gb|FL133540.1|FL133540
EST:     CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAG                         AATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
genomic: CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
EST: gi|148941362|gb|EC886271.2|EC886271
EST:     CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAG                         AATGCAGCTGA
genomic: CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGA
EST: gi|67016188|gb|CO444937.1|CO444937
EST:     CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAG                         AATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
genomic: CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTC
EST: gi|148940810|gb|EC885636.2|EC885636
EST:     CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAG                         AATGCAGCTGAT
genomic: CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGAT
EST: gi|149004197|gb|EE039006.2|EE039006
EST:     CAGTTGCTGGTAAGATGATCCGCATCAGGCGAGATGATCTTGCTACTCAG                         AATGCAGCTGAATGCAAA-GAGCGCACACCTATTGGAACATTGCAGAAGTT
genomic: CAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGA-TGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTT

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), 47 (downstream exon)
Score: 128

GCACAAATACGCTTTGTTGCCTATTATGAGATCGTACATTGATCATGCCGCAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 77

GCACAAATACGCTTTGTTGCCTATTATGAGATCGTACATTGATCATGCCGCAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

GCACAAATACGCTTTGTTGCCTATTATGAGATCGTACATTGATCATGCCGCAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 166

GCACAAATACGCTTTGTTGCCTATTATGAGATCGTACATTGATCATGCCGCAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACAAATACGCTTTGTTGCCTATTATGAGATCGTACATTGATCATGCCGCAGTTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtctgctgcattgtttattgtaaacagtatacgttcaaggttgtaggcagttcttgatttctaaattatcttaacactttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG