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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgccatagctacgcgtttcagattagttatactacctggtcgagttgagcatctatttaggccgagtaaacatctcatgtggcgatgctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG

Basic information

species Zea mays
transcript GRMZM2G113726_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113726_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 1
gcatgccatagctacgcgtttcagattagttatactacctggtcgagttgagcatctatttaggccgagtaaacatctcatgtggcgatgctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG
||||| ||| | |||  ||| ||||| |  | |         |||  |||   || | | |    |  | ||   | | |||||  |||  || |||||| |||||  |||| ||| |||||   ||||||||| ||||||||| ||| ||| || |||||||||||||| || | ||||||||||
gcatggcattgttacatgtt-cagataaactgttgaggggtctcgcattgtatatttgtatctagcatggaagt-tttgatgtgttgatcttgatgcagGTATGCACACCTGTAGATAAAGGGGCACTCTACTATGAGTTTCAGTACAACACAAGATCGGTGAAACCGACAATTCTTCATTTCCAG
















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|50330988|gb|CO526114.1|CO526114
EST:     GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAG                         GAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
genomic: GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
EST: gi|211202621|gb|FL195841.1|FL195841
EST:     GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAG                         GAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
genomic: GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
EST: gi|60349121|gb|DN216094.1|DN216094
EST:     GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAG                         GAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
genomic: GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
EST: gi|32795211|gb|CD947447.1|CD947447
EST:     GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAG                         GAATGCATGCCTGCAGAGAAAGACCAACTCTACTACGAGTTTCAGCACAGC
genomic: GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
EST: gi|71771227|gb|DR969164.1|DR969164
EST:     GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAG                         GAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC
genomic: GGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGC

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: 139

GAACGTGATGCCGACTACAAGGGACAAGTACAGGCAGTCACGGCTGCAGGGGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 348

GAACGTGATGCCGACTACAAGGGACAAGTACAGGCAGTCACGGCTGCAGGGGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

GAACGTGATGCCGACTACAAGGGACAAGTACAGGCAGTCACGGCTGCAGGGGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

GAACGTGATGCCGACTACAAGGGACAAGTACAGGCAGTCACGGCTGCAGGGGTACGCCAACTTTGAGAACGTGCCTAATTCCGGAAGGCTTTCTGAGAAGgcatgccata ... gctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttgagcatctatttaggccgagtaaacatctcatgtggcgatgctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG
         atctattta  TA-rich tract