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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgctcccgtacctcacctctcttttttgatggttccgtcctcttctgttggggtgcttgtcgaaggttctgaggcctgttgcttcgctttcatggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 2
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|37424637|gb|CF650051.1|CF650051
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTC
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTC
EST: gi|149027382|gb|EE046514.2|EE046514
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|88755472|gb|DY539613.1|DY539613
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|149058050|gb|EE156735.2|EE156735
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|87152120|gb|DY396909.1|DY396909
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|211353775|gb|FL303049.1|FL303049
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|5740519|gb|AI948209.1|AI948209
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|18450704|gb|BM428982.1|BM428982
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|78022867|gb|DV491254.1|DV491254
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
EST: gi|148996196|gb|EE035468.2|EE035468
EST:     CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAAC                         GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
genomic: CCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG

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: 118

GGACCTTGGCTCCGCGGCGGAGTCGGTGGCTGCTGACGAGGAGGCGCACGCCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 101

GGACCTTGGCTCCGCGGCGGAGTCGGTGGCTGCTGACGAGGAGGCGCACGCCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GGACCTTGGCTCCGCGGCGGAGTCGGTGGCTGCTGACGAGGAGGCGCACGCCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 62

GGACCTTGGCTCCGCGGCGGAGTCGGTGGCTGCTGACGAGGAGGCGCACGCCACGCCTCTCCACGAGATTGAGTCCCTTTGCATGCGCTGCGGCGAGAACgtgagtgctc ... atggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggggtgcttgtcgaaggttctgaggcctgttgcttcgctttcatggggttagGGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG
                                        ctttcat  CT-rich tract