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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctcatgctaaagcaaataattttgtttcggcagcaataatgaagatatttaccaatagcttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG

Basic information

species Zea mays
transcript GRMZM2G069976_T01
intron # 17
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|32838340|gb|CD978018.1|CD978018
EST:     CTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAG                         AAATGGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCA
genomic: CTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAGgtacctcatg ... ttttatgtagAAAT-GTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCA
EST: gi|71298058|gb|DR785006.1|DR785006
EST:     CTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAG                         AAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG
genomic: CTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAGgtacctcatg ... ttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG
EST: gi|32836585|gb|CD976263.1|CD976263
EST:     CTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAG                         AAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGGAAACATTCAG
genomic: CTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAGgtacctcatg ... ttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG

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: 35 (upstream exon), 45 (downstream exon)
Score: 52

CAAGGCAAATAGTACCCTGATGCAAATGGTAGGTGCTGACTGGATAAAATCTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAGgtacctcatg ... ttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG


Block sizes: 35 (upstream exon), 45 (downstream exon)
Score: 63

CAAGGCAAATAGTACCCTGATGCAAATGGTAGGTGCTGACTGGATAAAATCTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAGgtacctcatg ... ttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG


Block sizes: 35 (upstream exon), 45 (downstream exon)
Score: 79

CAAGGCAAATAGTACCCTGATGCAAATGGTAGGTGCTGACTGGATAAAATCTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAGgtacctcatg ... ttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG


Block sizes: 35 (upstream exon), 43 (downstream exon)
Score: 45

CAAGGCAAATAGTACCCTGATGCAAATGGTAGGTGCTGACTGGATAAAATCTGATAAGCGTGAGGATGATCTAGCTGGTCGCCCTGGGGGGCTAGTCCAGgtacctcatg ... ttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataattttgtttcggcagcaataatgaagatatttaccaatagcttttatgtagAAATGTGCAGCACAAGGGGGCACCCGATTCTTCTTCATTGTAAACATTCAG
                                            cttttat  CT-rich tract
                    aataatgaagatattt  TA-rich tract