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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagctcaagggagaagaaaagaactgcagagttgtcatcctccaatgatccgtatagctcgatttgttatttatacttattggcacacatcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCCATTCGGTTGATTTCTGG

Basic information

species Zea mays
transcript GRMZM2G089259_T01
intron # 12
splice site 3'
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|71428022|gb|DR809072.1|DR809072
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|60338197|gb|DN205170.1|DN205170
EST:     AGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|76012906|gb|DT940076.1|DT940076
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|50336815|gb|CO531941.1|CO531941
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|148994787|gb|EE034232.2|EE034232
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|60356662|gb|DN223635.1|DN223635
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|71329463|gb|DR801452.1|DR801452
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|29129794|gb|CB380498.1|CB380498
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG                         TGGGAACTCAGCGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
EST: gi|71321199|gb|DR797301.1|DR797301
EST:     AATGCTTTTGAGCTGGCAACATTCTTATGGTCTTTG                         TGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC
genomic: AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCC

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: 36 (upstream exon), 49 (downstream exon)
Score: 136

AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCCATTCGGTTGATTTCTGG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 31

AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCCATTCGGTTGATTTCTGG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 18

AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCCATTCGGTTGATTTCTGG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 57

AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTGgtgagaatct ... tcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCCATTCGGTTGATTTCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatccgtatagctcgatttgttatttatacttattggcacacatcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCCATTCGGTTGATTTCTGG
                 atttgttatttatact  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagctcaagggagaagaaaagaactgcagagttgtcatcctccaatgatccgtatagctcgatttgttatttatacttattggcacacatcttgtgcagTGGGAACTCAGTGCACAAACATGTTTCATGAAGCACTACTACATGGTTGCCATTCGGTTGATTTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - aagaaaa
- - - - - - - - - - - -actgcag
- - - - - - - - - - - - - - - - - - catcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacaca