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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctaatactgtacaccccgttcccaacttccatgcctctgacttctgttttaagtaatgtaagtctcgcaccctttaattattaatattctgtcctcttatttcattgttcgtcatggccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG

Basic information

species Zea mays
transcript GRMZM2G086484_T03
intron # 6
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|31351667|gb|CD436024.1|CD436024
EST:     GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG                         ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
genomic: GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
EST: gi|71311912|gb|DR792439.1|DR792439
EST:     GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG                         ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
genomic: GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
EST: gi|71762836|gb|DR960773.1|DR960773
EST:     GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG                         ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
genomic: GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
EST: gi|33091533|gb|CF051527.1|CF051527
EST:     GAAATCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG                         ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
genomic: GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
EST: gi|19770206|gb|BQ034927.1|BQ034927
EST:     GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG                         ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
genomic: GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
EST: gi|40334296|gb|CK368366.1|CK368366
EST:     GAAACCAAAATACTTCTGAAGCTTCAGCTGATGCAGATGAAG                         ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA
genomic: GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGA

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), 49 (downstream exon)
Score: 132

GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG


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

GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 35

GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAGgtatctaata ... ccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaattattaatattctgtcctcttatttcattgttcgtcatggccatgatcagATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG
      tattaat  putative branch site (score: 35)
     ttattaatattctgt  TA-rich tract