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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtctacaaatcgcagttacagctcatgacatttctatagaaacctgagtgccttaatttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG

Basic information

species Zea mays
transcript GRMZM2G011456_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 12
gtaagtgtctacaa-atcgcagttacagctcatgacatttctatagaaacctgagtgccttaatttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG
||||||| ||  |  ||  || | | | | | | | || | ||| ||      ||||  ||  |||   |||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| | |||||||||  |||||  |
gtaagtgcctctactatatcaatgataac-cgtaagatatttatggagtttgaagtgaattggtttatacagATCAAAGCACATAAAGATATTGCACATTTTGAAACTGCATATGTTGTCAAACTACACCGAATAGCAAGACTTGCACCAACACAATCG
















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|20803221|gb|BQ294271.1|BQ294271
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|21843268|gb|BQ703849.1|BQ703849
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|211483571|gb|FL225316.1|FL225316
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|60340216|gb|DN207189.1|DN207189
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|71300981|gb|DR786519.1|DR786519
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|26456816|gb|CA828399.1|CA828399
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|31558384|gb|CD527596.1|CD527596
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|37398225|gb|CF636423.1|CF636423
EST:     CATACACCAGGTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: CATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|26557923|gb|CA830158.1|CA830158
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|60397916|gb|DN230732.1|DN230732
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|71311076|gb|DR791852.1|DR791852
EST:     ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA
EST: gi|91048537|gb|EB158955.1|EB158955
EST:     CCAATAACAGCGTCAAAATTGCACGGCGAC                         ATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTT-TGAAA
genomic: CCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAA

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: 148

ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 83

ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 57

ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

ATACACCAGCTTCATCCAACCAATAACAGCGTCAAAATTGCACGACGACgtaagtgtct ... atttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcagttacagctcatgacatttctatagaaacctgagtgccttaatttccgcagATCAAAGCACACAAAGATATTGCACATTTTGAAACGGCATATGTTGTGAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG
                                        ccttaat  putative branch site (score: 89)
                                              tttccgc  CT-rich tract
                   atttctata  TA-rich tract