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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgcttggtcatgggagctcttctttgtacgtgcctaacatttgttgatgtaacatgcactgaattaactttgacatgtag

Basic information

species Zea mays
transcript GRMZM2G472625_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G33950.1 (Glycine max), 5'ss of exon 3
ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggt---gcttggtcatggg----agctcttctttgtacgtgcctaacatttgttgatgtaacatgcactgaattaactttgacatgtag-----------------------------
||||||||||||||||| |||||||| || || || || |||||||| || || ||||||||| ||    |    || ||       || |  |   ||| | | | |  | ||   || ||| |  |       |||   |   ||   | |                             
ACCATCAGTTACATGGCCGAACGTGTTGTTGGCACTGGATCATTTGGCATTGTTTTCCAGgtaaggataagtgaagtaattaccattaggtgataactgttcctactttgctttccctgctgtcaagtatctcatattgtttcacacccttgggttatgttcctttttgacctgaaacaaag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 3
ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatgg-tgcttggtca------tgggagctcttctttgtacg----------tgcctaacatttgttgatgtaacatgcactgaattaactttgacatgtag-----------
|||||||||||||||||||||||||| || || || || ||||||||  | || ||||||||| || ||     |||      ||  | || ||| || || |          || | |  || |  |  | |  ||  ||||| || |  |||  | | ||            
ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTCCAGgtaaggatgaacaatcaccaaggtgacaactattccttttaagctttctctgctgtcaagtatctcattgttttccac-cactggatgacatttctcttttacctaaaacatag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G09090.1 (Glycine max), 5'ss of exon 3
ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgcttggtcatgggagctcttctttgtacgtgcctaacatttgttgatgtaacatgcactgaattaactttgacatgtag
|| || ||||||||||||||||| || || || || || |||||||| || || |||||||||||||| |    ||         ||||||   | |||        |||   |   ||||||    ||||   |||  |   |||
ACTATTAGTTACATGGCAGAACGGGTTGTAGGAACTGGATCATTTGGAATTGTTTTCCAGgtatggtgat-aaccaactactagattctttactcttgc--------tgtcactaccacatgctgataatttgttttctctcttag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G15470.2 (Glycine max), 5'ss of exon 3
ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatgg-tgcttggtcatgggagctcttctttgtacgtgcctaacatttgttgatgtaacatgcactgaattaactttgacatgtag-----------------------------
|||||||||||||||||||||||||| || || || || ||||||||  | || || ||||||||| ||     |||    || |      | | | |    | | ||   || ||| ||||  |    |||   ||  ||   | |                             
ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAGgtatggatgaacaatcacct-agatgacaaatattcctattaagctttctctgctgtcacat--atctcattgttttccacccctggatggcattcctcttttacctaaaatatag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 3
ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgta--tggtgcttggtcatgggagctcttctttgtacgtgcctaacatttgttgatgtaacatgcactgaattaactttgacatgtag
|||||||||||||||||||| ||||| |||||||| || |||||||| || || || ||||||  |||   ||  | |||  | || ||   |||       | |  ||| || || |  ||||   ||  |   |  |    | |||
ACCATCAGTTACATGGCAGAGCGTGTTGTGGGTACCGGGTCATTTGGAATTGTTTTTCAGgtacatggatattaattatgcaaactatt---tgtgtcaatatcat-tttctttatatttcatgtcttggttcctcgcttctgt-tag

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|211126298|gb|FL137999.1|FL137999
EST:     ACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
genomic: ACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
EST: gi|20811237|gb|BQ295715.1|BQ295715
EST:     ACATGGCAGAACGTGTCG-GGGTACGGGCTCATTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
genomic: ACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
EST: gi|211127223|gb|FL138012.1|FL138012
EST:     ACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
genomic: ACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
EST: gi|211126301|gb|FL138002.1|FL138002
EST:     ACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
genomic: ACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
EST: gi|9825069|gb|BE575271.1|BE575271
EST:     TCGTCTTCCAG                         GCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG
genomic: TCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAG

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: 295

ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAGGATCGGCGTTACAAGAACCGGGAGCTGCAACTTATGCGTGCCATGGAGC


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 74

ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAGGATCGGCGTTACAAGAACCGGGAGCTGCAACTTATGCGTGCCATGGAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAGGATCGGCGTTACAAGAACCGGGAGCTGCAACTTATGCGTGCCATGGAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

ACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAGgtatggtgct ... tgacatgtagGCTAAGTGTTTGGAGACTGGAGAGACCTTCGCCATTAAGAAGGTGCTGCAGGATCGGCGTTACAAGAACCGGGAGCTGCAACTTATGCGTGCCATGGAGC