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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attccaataacatgccttgtgaatttaatggtgtcctgtcgatgcattttttccatactataatttgaagtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG

Basic information

species Zea mays
transcript GRMZM2G081653_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 3
--attccaataacatgccttgtgaatttaatggtgtcctgtcgatgcattttttccatactataatttgaa-gtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG
   | |  | |||||   |  |  | || |   |||   |   ||   |||| ||||||   |||  ||||  ||  |   | | |||||| | ||||  ||||||||||||||| | ||||| || || ||||| ||||||||||||||||| || |||||
ctctgcagaaaacatcattgttttactttaccatgtaaagctaatc--ttttgtccatatggtaagctgaatatgaattggtgggattttgaaatttt-gtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG
















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|89764107|gb|DY691035.1|DY691035
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTGATTGAG
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
EST: gi|149090139|gb|EE179439.2|EE179439
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
EST: gi|78079193|gb|DV507605.1|DV507605
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAAACACAGTATGATCATTTGCCACTAAATGAG
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG

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: 37 (upstream exon), 45 (downstream exon)
Score: 23

TAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTACCTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

TAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTACCTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 27

TAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTACCTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTACCTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttccatactataatttgaagtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG
                                           tatttttt  CT-rich tract
                               aatagcattttgtatt  TA-rich tract