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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatatcacattctagttttaggatctgtctgaccgatgttggcgatatattgattgcattgttcttaacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCATCCGAAGGATATGGTGAATGCATTAGGAACAGGAACAAACAATGAA

Basic information

species Zea mays
transcript GRMZM2G039889_T04
intron # 2
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|148952088|gb|EC897879.2|EC897879
EST:     CGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCT                         TATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCAT
genomic: CGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCTgtaagcatat ... aacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCAT
EST: gi|211416501|gb|FL082404.1|FL082404
EST:     CGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCT                         TATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTCCAACCAT
genomic: CGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCTgtaagcatat ... aacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCAT
EST: gi|91052439|gb|EB162857.1|EB162857
EST:     CGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCT                         TATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCAT
genomic: CGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCTgtaagcatat ... aacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCAT

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), 48 (downstream exon)
Score: 239

GCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCTgtaagcatat ... aacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCATCCGAAGGATATGGTGAATGCATTAGGAACAGGAACAAACAATGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 102

GCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCTgtaagcatat ... aacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCATCCGAAGGATATGGTGAATGCATTAGGAACAGGAACAAACAATGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 189

GCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCTgtaagcatat ... aacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCATCCGAAGGATATGGTGAATGCATTAGGAACAGGAACAAACAATGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 170

GCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCTgtaagcatat ... aacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCATCCGAAGGATATGGTGAATGCATTAGGAACAGGAACAAACAATGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgtctgaccgatgttggcgatatattgattgcattgttcttaacattgcagTATTTATTGAATAATAGATGTAAGTTTAAATCTAAATGCAAGTTCAACCATCCGAAGGATATGGTGAATGCATTAGGAACAGGAACAAACAATGAA
                                         tcttaac  putative branch site (score: 170)
                       atatattgatt  TA-rich tract