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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactactgctttttgggacaatgaatccttagaatatgaagttagcactctgtataatagtatgattttcatttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGATGTCGAGAAATCATTCACGGGGGTTACAGAGTCACTATCATCTTTGAGGA

Basic information

species Zea mays
transcript GRMZM2G126453_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 13
gtactactgctt-tttgggacaatgaatccttagaatatgaagtta-gcactctgtataatagtatgattttc---atttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGATGTCGAGAAATCATTCACGGGGGTTACAGAGTCACTATCATCTTTGAGGA
||||  |  ||| | |   ||   || |  |  |||||| || ||     || | |||  |   || ||| |    |||  |||||||||||| ||||| ||  ||||| |||| ||| |||||||||||||||||||||| |||||||||||||| ||  ||||||||||||| |||||||||||||
gtacagcctcttatctaaaactcagagttatccgaatataaatttgtattctttctattgtttcataattgtatggattgtctgtcagGTCATCTCAGAGGAACACAAAGCTGGCCCTATGATAGTGTTACTTAAGGATGTAGAGAAATCATTCACTGGAATTACAGAGTCACTTTCATCTTTGAGGA
















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|67031399|gb|CO460148.1|CO460148
EST:     TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAG                         GTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGAT
genomic: TTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactactgc ... ttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGAT




















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: 340

CTGAATTACTGCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactactgc ... ttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGATGTCGAGAAATCATTCACGGGGGTTACAGAGTCACTATCATCTTTGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

CTGAATTACTGCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactactgc ... ttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGATGTCGAGAAATCATTCACGGGGGTTACAGAGTCACTATCATCTTTGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

CTGAATTACTGCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactactgc ... ttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGATGTCGAGAAATCATTCACGGGGGTTACAGAGTCACTATCATCTTTGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 328

CTGAATTACTGCGCCCAGACTTTTCTGCTGGTGAAGAAGTTGAGAGGCTAGCTATGACCGAGTTAATAGAGgtactactgc ... ttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGATGTCGAGAAATCATTCACGGGGGTTACAGAGTCACTATCATCTTTGAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagaatatgaagttagcactctgtataatagtatgattttcatttcctgtcagGTCATTTCAGAAGAGAACAAATCTGGACCTCTGATAGTGTTACTTAAGGATGTCGAGAAATCATTCACGGGGGTTACAGAGTCACTATCATCTTTGAGGA
                                      ttttcatttcctgtc  CT-rich tract
                         tataatagtatgattt  TA-rich tract