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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaatctgtcattcttcacttagacccgtgatataagcaacatgaacacatgactgatggtgtgcgaaattcttgtcaacgacag

Basic information

species Zea mays
transcript GRMZM2G149224_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g29170.2 (Oryza sativa), 5'ss of exon 9
---------------------------------GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatg--aaaatctgtcattcttcacttagaccc-gtgatataagcaacatgaacacatgactgatggtgtgcgaaattcttgtcaacgacag
                                 ||   | | || ||  ||||||| ||||||||||||||||||||||| ||  ||||||||||||||||||||   |||  |  |  ||||    ||  | || |  | | ||| | ||||| ||||||||||||| ||  | |   |  ||   |  | ||
TGTGTCCAGTCTCTAACTGCTTGTTCTTGCCAGGTGGTATTCTCCCTATTGGTTGTGAGCATCCTTAGTTCCATGTCTTCGCAATCTGCATTTAAAATAGgtaattttaaataccatgcttctctttttgaatcctgcaaaacaaggagcatgagcacatgactgatgatgaactat-ctgatggggagaatag

upper sequence: GRMZM2G149224_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g29170.1 (Oryza sativa), 5'ss of exon 11
GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatg--aaaatctgtcattcttcacttaga-cccgtgatataagcaacatgaacacatgactgatggtgtgcgaaattcttgtcaacgacag
||   | | || ||  ||||||| ||||||||||||||||||||||| ||  ||||||||||||||||||||   |||  |  |  ||||    ||  | || |  | | ||| | ||||| ||||||||||||| ||  | |   |  ||   |  | ||
GTGGTATTCTCCCTATTGGTTGTGAGCATCCTTAGTTCCATGTCTTCGCAATCTGCATTTAAAATAGgtaattttaaataccatgcttctctttttgaatcctgcaaaacaaggagcatgagcacatgactgatgatgaactat-ctgatggggagaatag
















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|149072463|gb|EE160739.2|EE160739
EST:     GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG                         GTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
genomic: GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
EST: gi|211480846|gb|FL457134.1|FL457134
EST:     GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG                         GTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
genomic: GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
EST: gi|18650185|gb|BM499004.1|BM499004
EST:     GGTTGTCAGCATCCTTAGTTCTATGTCTTCTCAGTCTGCATTTAAAATAG                         GTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
genomic: GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
EST: gi|37381967|gb|CF627894.1|CF627894
EST:     GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG                         GTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
genomic: GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
EST: gi|31364078|gb|CD448433.1|CD448433
EST:     GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG                         GTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
genomic: GGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
EST: gi|211446981|gb|FL117889.1|FL117889
EST:     TCTCAGGCTGCATTTAAAATAG                         GTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA
genomic: TCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACA

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), 47 (downstream exon)
Score: 146

GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACAGCATTGATAGTATGGTGGGCGACGCCTGTACCATTCTTCTGCACTTTGG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 90

GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACAGCATTGATAGTATGGTGGGCGACGCCTGTACCATTCTTCTGCACTTTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 142

GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACAGCATTGATAGTATGGTGGGCGACGCCTGTACCATTCTTCTGCACTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAGgtaatgaaaa ... tcaacgacagGTACTGCTCTGGTTTTCACAGGCTTCAAAGCGTATGAGAAATGGGAGGACAGCATTGATAGTATGGTGGGCGACGCCTGTACCATTCTTCTGCACTTTGG