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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacatagtcttttaagtgtattgacatgttttttttctctgcaatcttctcctaacattgtttcatctgttaag

Basic information

species Zea mays
transcript GRMZM2G131998_T04
intron # 6
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|78091377|gb|DV519751.1|DV519751
EST:     GCATATCTGANAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT                         GTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
genomic: GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
EST: gi|13149651|gb|BG319973.1|BG319973
EST:     GCATATCTGAAAACCAGAGTTTTCTTATATCAGGYGGAGGTGATTCAACT                         GTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
genomic: GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
EST: gi|89761079|gb|DY689237.1|DY689237
EST:     CATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTNCA-CT                         GTTCGCCTGTGGGACTATGTAAATGGATGTC
genomic: CATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATT-CAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTC
EST: gi|71437750|gb|DR818800.1|DR818800
EST:     GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT                         GTTCGCCTGTGGGACTATG
genomic: GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATG
EST: gi|148973467|gb|EE024565.2|EE024565
EST:     GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT                         GTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
genomic: GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
EST: gi|78106892|gb|DV525310.1|DV525310
EST:     GCATATCTGANAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT                         GTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGAT
genomic: GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGAT
EST: gi|89759711|gb|DY688443.1|DY688443
EST:     GCATATCTGAAAACCAGAGTTTTCTTATATCANGAGGAGGTGATTCAACT                         GTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
genomic: GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCC
EST: gi|76017216|gb|DT944386.1|DT944386
EST:     GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT                         GTTCGCCTGTGGGACTAT
genomic: GCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTAT

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: 45 (upstream exon), 49 (downstream exon)
Score: 43

CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCCAAAGATAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 50

CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCCAAAGATAAG


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

CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCCAAAGATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 59

CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacat ... atctgttaagGTTCGCCTGTGGGACTATGTAAATGGATGTCTCCTTGATACATTTCAAGCCAAAGATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACTgtgggtacatagtcttttaagtgtattgacatgttttttttctctgcaatcttctcctaacattgtttcatctgttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG