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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaacttgtacaataatgccttacatgctatgttggttcttacccctaccctactttggcaaatgctttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTACTCATAGTAACAATGGTACTCGTCGTCGTCGTAATATGGCTAATAATCT

Basic information

species Zea mays
transcript GRMZM2G110143_T05
intron # 9
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|149070637|gb|EE159048.2|EE159048
EST:     TCAAGAGGTTTTGAATCAAATCATGAAATTCCAGATGGATTTCATGATTG                         TTTTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTA
genomic: TCAAGAGGTTCTGAATCAAATCATGAAATTCCAGATGGATCTCATGATTGgtaagaaaac ... tttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTA
EST: gi|149107882|gb|EE292242.2|EE292242
EST:     TCAAGAGGTTTTGAATCAAATCATGAAATTCCAGATGGATCTCATGATTG                         TTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTA
genomic: TCAAGAGGTTCTGAATCAAATCATGAAATTCCAGATGGATCTCATGATTGgtaagaaaac ... tttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTA

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), 49 (downstream exon)
Score: 154

GATGCTGATGCTGCTTACAGTGACCATCTTGATGCAGTCTATATTTTTGTTCAAGAGGTTCTGAATCAAATCATGAAATTCCAGATGGATCTCATGATTGgtaagaaaac ... tttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTACTCATAGTAACAATGGTACTCGTCGTCGTCGTAATATGGCTAATAATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

GATGCTGATGCTGCTTACAGTGACCATCTTGATGCAGTCTATATTTTTGTTCAAGAGGTTCTGAATCAAATCATGAAATTCCAGATGGATCTCATGATTGgtaagaaaac ... tttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTACTCATAGTAACAATGGTACTCGTCGTCGTCGTAATATGGCTAATAATCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 37

GATGCTGATGCTGCTTACAGTGACCATCTTGATGCAGTCTATATTTTTGTTCAAGAGGTTCTGAATCAAATCATGAAATTCCAGATGGATCTCATGATTGgtaagaaaac ... tttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTACTCATAGTAACAATGGTACTCGTCGTCGTCGTAATATGGCTAATAATCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

GATGCTGATGCTGCTTACAGTGACCATCTTGATGCAGTCTATATTTTTGTTCAAGAGGTTCTGAATCAAATCATGAAATTCCAGATGGATCTCATGATTGgtaagaaaac ... tttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTACTCATAGTAACAATGGTACTCGTCGTCGTCGTAATATGGCTAATAATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatgctatgttggttcttacccctaccctactttggcaaatgctttgcatcagTTCTAGTTGGAACAAGGTGCAGACTGGCAGAGATGCTGAGGGGTGTGTGTACTCATAGTAACAATGGTACTCGTCGTCGTCGTAATATGGCTAATAATCT
               ttcttac  putative branch site (score: 69)