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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgtctaaaaataccagctatagcttgtgacatttctgtataaacctgagtgacttgatttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG

Basic information

species Zea mays
transcript GRMZM2G169927_T03
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169927_T03 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 12
gtaggtgtctaaaa-ataccagctatagcttgtgacatttctgtataaacctgagtgacttgatttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG
||| ||| ||  |  ||| ||   ||| |  || | || | | |  |      ||||| ||| ||| | |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| | |||||||||  |||||  |
gtaagtgcctctactatatcaatgataacc-gtaagatatttatggagtttgaagtgaattggtttatacagATCAAAGCACATAAAGATATTGCACATTTTGAAACTGCATATGTTGTCAAACTACACCGAATAGCAAGACTTGCACCAACACAATCG
















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|211483572|gb|FL225317.1|FL225317
EST:     AATAACAGCATCAAAATTGCACAACGAT                         ATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAA
genomic: AATAACAGCATCAAAATTGCACAACGATgtaggtgtct ... atttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAA
EST: gi|211483570|gb|FL225315.1|FL225315
EST:     ATACACCAGCTTCATCCAACCAATAACAGCATCAAAATTGCACAACGAT                         ATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAA
genomic: ATACACCAGCTTCATCCAACCAATAACAGCATCAAAATTGCACAACGATgtaggtgtct ... atttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAA

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: 44 (upstream exon), 49 (downstream exon)
Score: 142

ATACACCAGCTTCATCCAACCAATAACAGCATCAAAATTGCACAACGATgtaggtgtct ... atttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 74

ATACACCAGCTTCATCCAACCAATAACAGCATCAAAATTGCACAACGATgtaggtgtct ... atttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 83

ATACACCAGCTTCATCCAACCAATAACAGCATCAAAATTGCACAACGATgtaggtgtct ... atttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 100

ATACACCAGCTTCATCCAACCAATAACAGCATCAAAATTGCACAACGATgtaggtgtct ... atttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accagctatagcttgtgacatttctgtataaacctgagtgacttgatttctgcagATCAAAGCACACAAAGACATTGCACATTTTGAAACCGCATATGTTGTCAAACTACACCGCATAGCGACACTTGCACCTCCACAACAG
                                        acttgat  putative branch site (score: 100)
                                              tttctgc  CT-rich tract
                        tgtataaa  TA-rich tract