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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcattgcaacccagtcttgcgcatgacagttcgctggagctgcaggttctcacagaatctctccatcctggggtgtcgatcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTACTCTTCTTTGAACCTCGATACGGTCAGACTAACATCCTGATATATCTGGG

Basic information

species Zea mays
transcript GRMZM2G461791_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461791_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g50180.1 (Oryza sativa), 3'ss of exon 4
gtgagtcattgcaacccagtcttgcg-catgacagttcgctggagctgcaggttctcacagaatctctc----catcctggggtgtcgatcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTACTCTTCTTTGAACCTCGATACGGTCAGACTAACATCCTGATATATCTGGG
|| ||||| ||  || || |  |||  ||    | |  |    ||||  |    || |||   | ||||    |||  || ||| || | ||    |||| |||||| |||||| |||  || | ||  || | |||| ||| ||||| |||||||||||||||||||| |||||||| || ||| |||||||||||||
gttagtcactgacacacatttctgcaacactgta-taggtcacagctatataa-ctaacatgctttctctgaacatattgtggtttcaa-cacctccagGATTTCTAACATATGCGGTAGCAACCTTAGTAGTCGTGGCAGCACTAGTTCTCTTCTTTGAACCTCGATATGGTCAGACAAATATCATGATATATCTGGG
















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|32801086|gb|CD953322.1|CD953322
EST:     GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAG                         GGTTTCTAGCATGTGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
genomic: GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
EST: gi|32798698|gb|CD950934.1|CD950934
EST:     GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAG                         GGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
genomic: GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
EST: gi|21481199|gb|BQ577882.1|BQ577882
EST:     GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAG                         GGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
genomic: GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
EST: gi|26455492|gb|CA827075.1|CA827075
EST:     GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAG                         GGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAG
genomic: GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAG
EST: gi|21391006|gb|BQ529055.1|BQ529055
EST:     GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAG                         GGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
genomic: GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
EST: gi|87154688|gb|DY399477.1|DY399477
EST:     GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAG                         GGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC
genomic: GCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTAC

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), 48 (downstream exon)
Score: 71

GTGTCGTGCATAGTAGGTTCAGTTGTTGTTGTCATGCATGCTCCTGAAGAGCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTACTCTTCTTTGAACCTCGATACGGTCAGACTAACATCCTGATATATCTGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

GTGTCGTGCATAGTAGGTTCAGTTGTTGTTGTCATGCATGCTCCTGAAGAGCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTACTCTTCTTTGAACCTCGATACGGTCAGACTAACATCCTGATATATCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GTGTCGTGCATAGTAGGTTCAGTTGTTGTTGTCATGCATGCTCCTGAAGAGCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTACTCTTCTTTGAACCTCGATACGGTCAGACTAACATCCTGATATATCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 33

GTGTCGTGCATAGTAGGTTCAGTTGTTGTTGTCATGCATGCTCCTGAAGAGCATATGCCTAACTCTGTCAAGGAAATCTGGAACCTAGCTACTCAACCAGgtgagtcatt ... tcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTACTCTTCTTTGAACCTCGATACGGTCAGACTAACATCCTGATATATCTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagctgcaggttctcacagaatctctccatcctggggtgtcgatcattggcagGGTTTCTAGCATATGTGGTGACAGCATTGTTACTTGTGGGAGCGCTAGTACTCTTCTTTGAACCTCGATACGGTCAGACTAACATCCTGATATATCTGGG
            ttctcac  putative branch site (score: 33)