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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttctttacccactttttcgttctacgcatgtcattttgtggtatatcatatatgtattcttcttaggaaaaacattcagagcatatctttgttaagtctgaattttcattgccatttattttgatgcag

Basic information

species Zea mays
transcript GRMZM2G051842_T02
intron # 4
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|71446345|gb|DR827395.1|DR827395
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|60338856|gb|DN205829.1|DN205829
EST:     ACAGGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: ACAGGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|91057161|gb|EB167579.1|EB167579
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|76293563|gb|DV033131.1|DV033131
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|76286678|gb|DV026246.1|DV026246
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCCAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|71771409|gb|DR969346.1|DR969346
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|78105422|gb|DV523840.1|DV523840
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|148987163|gb|EE030992.2|EE030992
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|71447665|gb|DR828715.1|DR828715
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|78103938|gb|DV522356.1|DV522356
EST:     AAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: AAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|149088934|gb|EE178077.2|EE178077
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|148959742|gb|EC905640.2|EC905640
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT

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), 39 (downstream exon)
Score: 277

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 65

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 99

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 130

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttctttacccactttttcgttctacgcatgtcattttgtggtatatcatatatgtattcttcttaggaaaaacattcagagcatatctttgttaagtctgaattttcattgccatttattttgatgcag

- - - - - - -  AAGGAG
- - - - - - - -  GGAGGA
- - - - - - - - - GAGGAT