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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcatgcaatcaatgtccacgtcacatacgcgcaggcacagaactgaatgagcatatatttctcgtgattactgtcatctcaaggttctattatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT

Basic information

species Zea mays
transcript GRMZM2G138676_T05
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138676_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 10
ggcatgcaatcaatgtccacgtcacatacgcg--caggcacagaactgaatgagcatatatttctcgtgattactgtcatctcaaggttctattat--atccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT
    ||  | |||||||||  | |  |  | |  ||     | || | ||  |  |  |  |    ||  ||  ||| |    || ||| | || |  | ||||||||| |||| |||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||| |||
---gtgtgagcaatgtccatattatgtgtgtgttcaattggaaaattaaacaa-tactttctcactgttctttttgtaactcaaaagttttgttttttacccagGTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGGACCTTGTAAGCAGGTTTCTGCAATACTCACCAAATCTTCGGTGCACCGCT
















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|38229772|gb|CF920085.1|CF920085
EST:     ACTACACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG                         GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT
genomic: ACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTT




















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: 47 (upstream exon), 49 (downstream exon)
Score: 102

GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT


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

GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 106

GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 80

GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaata ... ttatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgagcatatatttctcgtgattactgtcatctcaaggttctattatatccagGTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT
                                        ttctatt  CT-rich tract
                                        ttctattatat  TA-rich tract