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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttgatgctttggcatgttagtctgtaaaagaatcttcactgcggctactaatactgtcaaaccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG

Basic information

species Zea mays
transcript GRMZM2G142334_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 13
gttagcttgatgctttg--gcatgtt--agtctgtaaaagaatcttcactgcggctactaatactgtcaaaccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG
|||| ||| ||| | ||  |||||||  | | |||| |||  || ||| | |  ||||||||  ||  || ||||| |||||||  || ||||| |||||||| ||||||||||||||||| |||||||||||||||||||||||| | || ||||||||||| |||||| ||||||||||
gttaccttcatgatgtgtagcatgtttaactttgtagaagc-tcgtcatttcaactactaattttg--aatccttatgcagGTGCTGAAAGCACCGGAATAGAGGCCAATGGAAATTCCTACGATCTGAGCACAAAGTTGCTCCATCTCGCATGGCACCCATCCGAAAATTTAATTGCTTG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 13
----------------------gttagcttgatgctttggcatgttagtctgtaaaagaatcttcactgcggc-tactaatactgtcaaacct-tacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG
                        ||| |   |   ||   |    | | |||| ||||  |   |    | | |  ||    |  ||   || |    |||   ||| ||  |||||   ||  | ||||||||  | | |||| | |  ||||||||||||||||| |||||||| ||| |||||||     | |||||
cgaatttcaattccactttgtgagtagatcattcaatttttagagcaat-tgtagaagacccagaaaactgacatgttagggattccatttctgtgaaaagGAACAGATAGTTCTGGAGCTGACACAAATGGAAACGCTTTTGATTTCATGACAAAGTTGCTCCATTTAGCCTGGCATCCAACTGAAAACTCCCTAGCTTG
















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|120481038|gb|EH211133.1|EH211133
EST:     CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAG                         GTGGAGAGAGCACTGTAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
genomic: CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
EST: gi|67016408|gb|CO445157.1|CO445157
EST:     CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAG                         GTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTTTGATCTGAGCA
genomic: CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
EST: gi|71417754|gb|DR804198.1|DR804198
EST:     CTCTAGAGCTACCAGATCCTTAAGTACTCTGACAAGGGCCGTTAGACGAG                         GTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
genomic: CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
EST: gi|211530906|gb|FL193982.1|FL193982
EST:     CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAG                         GTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
genomic: CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
EST: gi|6012734|gb|AW062171.1|AW062171
EST:     CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAG                         GTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
genomic: CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
EST: gi|211530907|gb|FL193983.1|FL193983
EST:     CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAG                         GTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA
genomic: CTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCA

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: 79

GCGGCAGGTCCAGACTACCTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 59

GCGGCAGGTCCAGACTACCTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GCGGCAGGTCCAGACTACCTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

GCGGCAGGTCCAGACTACCTCTAGAGCTACCAGATCCCTAAGTACTCTGACAAGGGCCGTTAGACGAGgttagcttga ... ccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtctgtaaaagaatcttcactgcggctactaatactgtcaaaccttacgcagGTGGAGAGAGCACTGGAATAGATGCCAATGGAAATTCCTATGATCTGAGCACAAAGTTGCTCCATTTGGCCTGGCACCCATCTGAAAATCTAATTGCTTG
        taaaagaat  TA-rich tract