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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtgttgtctggtggattgagttgattttttcttgatgtatgtagttcctgacaatttccacattttgtcgtgacag

Basic information

species Zea mays
transcript GRMZM2G173777_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173777_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g07070.1 (Oryza sativa), 5'ss of exon 12
GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtgttgtctggtggattgagttgattttttcttgatgtatgtagttcctgacaatttccacattttgtcgtgacag
||||| |||||||||||||||||||||||||||||||| ||||||||||| ||| | ||||| ||||| |||||||||| ||         |||||||    ||   ||||||| |     |||      | ||  |||    | |||  ||
GACATTCGCCTTGTTCGGGATAAGTTTACTCATGTGTCCAGAGGTTTTGCTTTCATCCATTTTCATTCAgtaagtagtggtgggaaaaatgttgagtt----ttcctttgatgtctac---tcccatatttatctgcatccaattgtgttag
















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|211224726|gb|FL222444.1|FL222444
EST:     ATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG                         GTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAG
genomic: ATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtg ... gtcgtgacagGTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAG
EST: gi|211344311|gb|FL081282.1|FL081282
EST:     ATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG                         GTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAG
genomic: ATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtg ... gtcgtgacagGTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAG
EST: gi|13490949|gb|BG517713.1|BG517713
EST:     ATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG                         GTGGAAGATGCTACGAAAGCTCTGGAAG-NNNNNNNGGGATTACACTTGAG
genomic: ATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtg ... gtcgtgacagGTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAG

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: 208

GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtg ... gtcgtgacagGTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAGAAAAACGGTCAGGTTTTGCGTGTAGCATATGCTAAAAGTACACATGGAC


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

GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtg ... gtcgtgacagGTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAGAAAAACGGTCAGGTTTTGCGTGTAGCATATGCTAAAAGTACACATGGAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 167

GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtg ... gtcgtgacagGTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAGAAAAACGGTCAGGTTTTGCGTGTAGCATATGCTAAAAGTACACATGGAC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 168

GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCGgtaagtagtg ... gtcgtgacagGTGGAAGATGCTACGAAAGCTCTGGAAGCTACAAACGGGATTACACTTGAGAAAAACGGTCAGGTTTTGCGTGTAGCATATGCTAAAAGTACACATGGAC