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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcactacggcggcggggctgcagcctctgcgtttactatggtagcctcctgcttatgcgtagtaatgtatattctccctacttgtttgagaattattttcatatcataattttttttccttagctgagagcctgagacaaacgatctctctgatcgaatttgctcatctgtgttctcttccaattccaacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 1
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|71771533|gb|DR969470.1|DR969470
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGGCAG                      
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCC-A---AGgtatgcacta ... caacatg
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|29946549|gb|CB816205.1|CB816205
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|148957215|gb|EC903225.2|EC903225
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAG                         GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
genomic: TCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG

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), 45 (downstream exon)
Score: 70

GGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

GGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 185

GGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

GGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTCCGTCTGCCGCAGCGACGTCACTGCCTGGCAATCCAAGgtatgcacta ... caacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatctctctgatcgaatttgctcatctgtgttctcttccaattccaacatgcagGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG
      ctctgat  putative branch site (score: 196)
                               ttctcttccaattcc  putative PPT
               aattt  TA-rich tract