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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgcaagttcctcaggtttgagttgagcccgtcgttcagcaaacctcttctgatttctaaatttagcacggcctccaatcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCTTCGGTGCTGGCCTCGTCGTATCATGCTCCTAAATTTTCGAACGATATAT

Basic information

species Zea mays
transcript GRMZM2G129147_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|29945401|gb|CB815620.1|CB815620
EST:     TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAG                         ATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
genomic: TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
EST: gi|6022134|gb|AW067062.1|AW067062
EST:     TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAG                         ATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
genomic: TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
EST: gi|211335730|gb|FL462838.1|FL462838
EST:     TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAG                         ATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
genomic: TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
EST: gi|71313691|gb|DR793426.1|DR793426
EST:     TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAG                         ATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
genomic: TCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
EST: gi|113831665|gb|DW948279.1|DW948279
EST:     ATCGCCGGGTGGAATACCGTCGAG                         ATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT
genomic: ATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCT

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 51

GCCTCGGCTTCTCGGCCACCCAGCTCTCCATCTCCATTCCCATGGCGACCTCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCTTCGGTGCTGGCCTCGTCGTATCATGCTCCTAAATTTTCGAACGATATAT


Block sizes: 19 (upstream exon), 33 (downstream exon)
Score: 3

GCCTCGGCTTCTCGGCCACCCAGCTCTCCATCTCCATTCCCATGGCGACCTCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCTTCGGTGCTGGCCTCGTCGTATCATGCTCCTAAATTTTCGAACGATATAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 3

GCCTCGGCTTCTCGGCCACCCAGCTCTCCATCTCCATTCCCATGGCGACCTCCGACTTCTCCAACACCAGCTCCAGATCGCCGGGTGGAATACCGTCGAGgtaagcgcaa ... atcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCTTCGGTGCTGGCCTCGTCGTATCATGCTCCTAAATTTTCGAACGATATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttcagcaaacctcttctgatttctaaatttagcacggcctccaatcattgcagATGAACGAGTACCGTGCATGTGGATCCCAGCGTCTTAGGGTTGACGACTCTTCGGTGCTGGCCTCGTCGTATCATGCTCCTAAATTTTCGAACGATATAT
                      ttctaaa  putative branch site (score: 3)
                  tgatttctaaattta  TA-rich tract