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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCAAAGAAATAGCACCTGTGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtgattttaaggtttcttatgtcacgtttcatttaaaatttcaactaaatggctagttttccccccttcacattgacag

Basic information

species Zea mays
transcript GRMZM2G376731_T01
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 24
lower sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 24
ATTGGCAAAGAAATAGCACCTGTGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtg-attttaaggt-ttcttatgtcacgtttcatttaaa-----atttcaactaaatggctagttttccccccttcacattgacag
||||||||||||||  |||||||||| ||||| |||||||| |||||| |  | ||  ||||||| || |||||   || |||||||| | |||| ||  |   ||| | |  |      |||||| ||||||| || || |  ||      ||  | ||||
ATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAGgtaattgcattttaagttgttctcatcacgtcttttactcgagtgagcatttcagctaaatgcctcgtgtgtcctgacatactattacag
















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|30306910|gb|CD001583.1|CD001583
EST:     TGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAG                         GGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTT
genomic: TGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtgatt ... acattgacagGGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTT
EST: gi|32856540|gb|CD996221.1|CD996221
EST:     TGGTGATCACCGTTGTTTCGTGCTTGATTACCATTCTAAAATCCCCAGAG                         GGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTT
genomic: TGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtgatt ... acattgacagGGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTT

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), 47 (downstream exon)
Score: 97

ATTGGCAAAGAAATAGCACCTGTGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtgatt ... acattgacagGGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTTAGCTGGGTCTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

ATTGGCAAAGAAATAGCACCTGTGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtgatt ... acattgacagGGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTTAGCTGGGTCTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

ATTGGCAAAGAAATAGCACCTGTGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtgatt ... acattgacagGGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTTAGCTGGGTCTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 88

ATTGGCAAAGAAATAGCACCTGTGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAGgtgggtgatt ... acattgacagGGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTTAGCTGGGTCTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC