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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatttggacatgctgtagcagactgatattctgtactgctaatgaaaccttttcttttttttgtttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT

Basic information

species Zea mays
transcript GRMZM2G018508_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 23
gtaagaatttggacatgctgt----agcagac--tgatattctgtactgctaatgaaaccttttcttttttttgtttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT
||||| || | |||||||| |    ||   |   | ||||| |||| | | | ||| |  ||||||||  | | ||| | |||||||| |||  |||||| |||||| |||| |||||||| || ||| |||||||||| || ||||||||| | ||||||||||||||||| ||||| ||||||
gtaagcatctcgacatgctatgattagtgaatcttaatattttgtattaccactgatattttttctttgctgt-tttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACTTGGTGTTGATGACCCAACTAAAATTCGGCTTACATCGCATAACTGTTAT
















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|37375031|gb|CF623926.1|CF623926
EST:     CACTTTCGTTCACTGGAGAAGCCCAAGGAGGACGATTTTTTCCTCGAGAT                         GTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACT
genomic: CACTTTCGTTCACTGGAGAAGCCCAAGGAGGACGATTTTTTCCTCGAGATgtaagaattt ... ttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACT
EST: gi|40286963|gb|CK327355.1|CK327355
EST:     CACTTTCGTTCACTGGAGGAGCCCAAGGAGGACGANNNNNNNCTCGAGAT                         GTCAAAGATTTTCACATATGATCAAGTCGCGGAAAAAGTAGCTGAAAAACT
genomic: CACTTTCGTTCACTGGAGAAGCCCAAGGAGGACGATTTTTTCCTCGAGATgtaagaattt ... ttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACT

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: 375

GTGGTCCACTTTCGTTCACTGGAGAAGCCCAAGGAGGACGATTTTTTCCTCGAGATgtaagaattt ... ttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

GTGGTCCACTTTCGTTCACTGGAGAAGCCCAAGGAGGACGATTTTTTCCTCGAGATgtaagaattt ... ttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

GTGGTCCACTTTCGTTCACTGGAGAAGCCCAAGGAGGACGATTTTTTCCTCGAGATgtaagaattt ... ttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

GTGGTCCACTTTCGTTCACTGGAGAAGCCCAAGGAGGACGATTTTTTCCTCGAGATgtaagaattt ... ttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactgatattctgtactgctaatgaaaccttttcttttttttgtttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT
                 tgctaat  putative branch site (score: 377)
                            ccttttcttttttttg  putative PPT
                    taatgaaaccttttct  TA-rich tract