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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgttctgtctctcgtacttcagtttatgttgcacttttgttttcgatcacctgttacccttctgagatttgtgattatcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTCGTGCGAGGGCTGCCTCTGCCTTCCCCACTGATAAGCCAAACTCGCATAA

Basic information

species Zea mays
transcript GRMZM2G115304_T01
intron # 4
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|211443582|gb|FL163986.1|FL163986
EST:     TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAG                         GNTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTC
genomic: TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTC
EST: gi|87153485|gb|DY398274.1|DY398274
EST:     TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAG                         GGTCTGCTGAGCAGAGTTTTG
genomic: TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTG
EST: gi|149113041|gb|EE295814.2|EE295814
EST:     TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAG                         GGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTC
genomic: TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTC
EST: gi|18649087|gb|BM497906.1|BM497906
EST:     TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAG                         GGTCTGCTGAGCAGAGTTTTGC
genomic: TGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTGC

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), 46 (downstream exon)
Score: 36

GTTCTAGCAACAATTTGTGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTCGTGCGAGGGCTGCCTCTGCCTTCCCCACTGATAAGCCAAACTCGCATAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 22

GTTCTAGCAACAATTTGTGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTCGTGCGAGGGCTGCCTCTGCCTTCCCCACTGATAAGCCAAACTCGCATAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 24

GTTCTAGCAACAATTTGTGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTCGTGCGAGGGCTGCCTCTGCCTTCCCCACTGATAAGCCAAACTCGCATAA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 25

GTTCTAGCAACAATTTGTGAAGAGCTCTCTCAAGATAGCATTTTACTCATCTATATATCAGCGTCAGgttagttgtt ... atcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTCGTGCGAGGGCTGCCTCTGCCTTCCCCACTGATAAGCCAAACTCGCATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttttgttttcgatcacctgttacccttctgagatttgtgattatcttgttagGGTCTGCTGAGCAGAGTTTTGCTAGTCAAAAGTTTGGCTCTAGCTCATCTCGTGCGAGGGCTGCCTCTGCCTTCCCCACTGATAAGCCAAACTCGCATAA
                                           ttatctt  CT-rich tract
                                          attatctt  TA-rich tract