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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAAGGATGCCATCTTTAAGACTCTGATTGCAAATGGAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatatagatcaagattcatcacaatgtcactattataatatgatatctatcaccttcataacgaccttatcgctcattgcctcattcaattcattggctgtgatttatcaagtgaag

Basic information

species Zea mays
transcript GRMZM2G108416_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g24460.3 (Oryza sativa), 5'ss of exon 11
ATTAAGGATGCCATCTTTAAGACTCTGATTGCAAATGGAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaat-atagatcaagattcatca-caatgtcactattataatatg-atatctatcaccttcataacgaccttatcgctcattgcctcattcaattcattggctgtgatttatcaagtgaag
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ATTAAGGATGCCATCTTTAGGACTCTCAATGCAAATGGAATGTTCAATAATGCTCATATAAGGCTTACACTCACCCGTGGGAAGAAGgtaaaaagatgaacctagattcatcagtagtgtcacttttcaagtatatatatttgtcgacatctttgc-atatcctgcttgatcacttcattcgctaccttcaatttca---aaaaactgcag
















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|78087292|gb|DV515685.1|DV515685
EST:     ATGTTTTCA-CA-TGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAG                         GTGACATCTGGAATG
genomic: ATGTT--CAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatata ... tcaagtgaagGTGACATCTGGAATG
EST: gi|211301117|gb|FL169205.1|FL169205
EST:     GAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAG                         GTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATT
genomic: GAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatata ... tcaagtgaagGTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATT
EST: gi|78115926|gb|DV534314.1|DV534314
EST:     GAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAG                         GTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATT
genomic: GAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatata ... tcaagtgaagGTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATT

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), 48 (downstream exon)
Score: 138

ATTAAGGATGCCATCTTTAAGACTCTGATTGCAAATGGAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatata ... tcaagtgaagGTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 134

ATTAAGGATGCCATCTTTAAGACTCTGATTGCAAATGGAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatata ... tcaagtgaagGTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

ATTAAGGATGCCATCTTTAAGACTCTGATTGCAAATGGAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatata ... tcaagtgaagGTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 159

ATTAAGGATGCCATCTTTAAGACTCTGATTGCAAATGGAATGTTCAACAATGCTCATATAAGGCTCACGCTCACCCGTGGGAAAAAGgtaaaatata ... tcaagtgaagGTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATTG