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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctgctttttaggacaaggaatcctgttgaatatgaagttatcactctgtatgatagtatgattttcattttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAGTTACCGAGTCACTTTCATCTTTGCGGA

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 13
gtactgctgctt-tttaggacaaggaatcctgttgaatatgaagttat-cactctgtatgatagtatgattttc---attttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAGTTACCGAGTCACTTTCATCTTTGCGGA
|||| ||  ||| | ||  ||   || |  |   |||||| || || |   || | |||  |   || ||| |    ||| ||||||||||||| ||||| ||  ||||| |||| ||| |||| |||||||||||||||||||||||||||||||||||| |||| |||||||||||||||||| |||
gtacagcctcttatctaaaactcagagttat-ccgaatataaatttgtattctttctattgtttcataattgtatggattgtctgtcagGTCATCTCAGAGGAACACAAAGCTGGCCCTATGATAGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAATTACAGAGTCACTTTCATCTTTGAGGA
















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|6994163|gb|AW453377.1|AW453377
EST:     TTTCTGCTGGTGAAGAAGGTGAGAGGCTAGCTATGACCGAGTTAATAGAG                         GGCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGGGGTACTTAAGGAT
genomic: TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
EST: gi|211048842|gb|FL187602.1|FL187602
EST:     TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAG                         GTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
genomic: TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
EST: gi|211048840|gb|FL187600.1|FL187600
EST:     TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAG                         GTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
genomic: TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
EST: gi|211048843|gb|FL187603.1|FL187603
EST:     TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAG                         GTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
genomic: TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
EST: gi|211051789|gb|FL187607.1|FL187607
EST:     TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAG                         GTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
genomic: TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGAT
EST: gi|211048844|gb|FL187604.1|FL187604
EST:     TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAG                         GTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGA
genomic: TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGA

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: 303

CTGAATCACTTCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAGTTACCGAGTCACTTTCATCTTTGCGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 294

CTGAATCACTTCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAGTTACCGAGTCACTTTCATCTTTGCGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 332

CTGAATCACTTCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAGTTACCGAGTCACTTTCATCTTTGCGGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 284

CTGAATCACTTCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactgctgc ... tttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAGTTACCGAGTCACTTTCATCTTTGCGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgaatatgaagttatcactctgtatgatagtatgattttcattttctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATTGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAGTTACCGAGTCACTTTCATCTTTGCGGA
                                      ttttcattttctgtc  CT-rich tract
                                 tatgattttcatttt  TA-rich tract