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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactattcaatttgttcatgatctgaaaattctcacaggaatacttactgccttttgatatcgacacatgttgttctttcttcagATGACAGTAAATCGACTTGAGCTAGTTGAG

Basic information

species Zea mays
transcript GRMZM5G807582_T02
intron # 5
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|161587495|gb|EY961062.1|EY961062
EST:     AAATTAAAGCACTTGAGACCTTAGTAAATGGCACAAATGAAGAAAATGAG                         ATGACAGTAAATCGACTTGAGCTAGTTGAGG
genomic: AAATTAAAGCACTCGAGACCTTAGTAAATGGCACAAATGAAGAAAATGAGgtaactattc ... ctttcttcagATGACAGTAAATCGACTTGAGCTAGTTGAGG




















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: 47 (upstream exon), 49 (downstream exon)
Score: 444

CAAAATAGCATCATCAAGACCCGGGAAGACAAGTACCGTTCAAAAATTAAAGCACTCGAGACCTTAGTAAATGGCACAAATGAAGAAAATGAGgtaactattc ... ctttcttcagATGACAGTAAATCGACTTGAGCTAGTTGAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 70

CAAAATAGCATCATCAAGACCCGGGAAGACAAGTACCGTTCAAAAATTAAAGCACTCGAGACCTTAGTAAATGGCACAAATGAAGAAAATGAGgtaactattc ... ctttcttcagATGACAGTAAATCGACTTGAGCTAGTTGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 21

CAAAATAGCATCATCAAGACCCGGGAAGACAAGTACCGTTCAAAAATTAAAGCACTCGAGACCTTAGTAAATGGCACAAATGAAGAAAATGAGgtaactattc ... ctttcttcagATGACAGTAAATCGACTTGAGCTAGTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

CAAAATAGCATCATCAAGACCCGGGAAGACAAGTACCGTTCAAAAATTAAAGCACTCGAGACCTTAGTAAATGGCACAAATGAAGAAAATGAGgtaactattc ... ctttcttcagATGACAGTAAATCGACTTGAGCTAGTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcacaggaatacttactgccttttgatatcgacacatgttgttctttcttcagATGACAGTAAATCGACTTGAGCTAGTTGAG
                                      tgttgttctttcttc  CT-rich tract
                      ttttgatat  TA-rich tract