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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcagcattctctactttttagccttactaccagcaagtctaacctggaacgcgtcatgcttaatatcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCAGTCCCCGGGGCTTTCAGTACTCCCTTGGCAGAAACATGCAATGAAGTTG

Basic information

species Zea mays
transcript GRMZM2G136624_T03
intron # 10
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|60340696|gb|DN207669.1|DN207669
EST:     CAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAG                         ATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCA
genomic: CAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAGgtaatcagca ... tcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCA
EST: gi|60345916|gb|DN212889.1|DN212889
EST:     CAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAG                         ATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCA
genomic: CAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAGgtaatcagca ... tcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 146

CGTTCAAGAGTATCCAATCACCACCGAGGAAAACGAAGACAAGGACGAGCCAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAGgtaatcagca ... tcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCAGTCCCCGGGGCTTTCAGTACTCCCTTGGCAGAAACATGCAATGAAGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 19

CGTTCAAGAGTATCCAATCACCACCGAGGAAAACGAAGACAAGGACGAGCCAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAGgtaatcagca ... tcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCAGTCCCCGGGGCTTTCAGTACTCCCTTGGCAGAAACATGCAATGAAGTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 16

CGTTCAAGAGTATCCAATCACCACCGAGGAAAACGAAGACAAGGACGAGCCAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAGgtaatcagca ... tcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCAGTCCCCGGGGCTTTCAGTACTCCCTTGGCAGAAACATGCAATGAAGTTG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 24

CGTTCAAGAGTATCCAATCACCACCGAGGAAAACGAAGACAAGGACGAGCCAGATATGCTTGTGGACTTGTCACCGTACAAGGAAGATGGCTCCTTGGAGgtaatcagca ... tcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCAGTCCCCGGGGCTTTCAGTACTCCCTTGGCAGAAACATGCAATGAAGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttactaccagcaagtctaacctggaacgcgtcatgcttaatatcttctgcagATCGAGTACTCTTCACTTCTTGATGTAAGGCTACTGAAGGGTATTGAACCAGTCCCCGGGGCTTTCAGTACTCCCTTGGCAGAAACATGCAATGAAGTTG
                                           tatcttct  CT-rich tract
 ttaatatctt  TA-rich tract