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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcgtgatttcacccaaaatgactcaggatcctttggttttatactgtcactgtgcactgccttactctgttgctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAGCTTGACAAACTCATATGTACCTATCCTTGGAACAATTCCGAACTGACAG

Basic information

species Zea mays
transcript GRMZM2G156638_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156638_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g51370.2 (Oryza sativa), 3'ss of exon 9
gtaagttctcgtgatttcacccaaaatgactcaggatcctttggttttatactgtcactgtgcactgccttactctgt-tgctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAGCTTGACAAACTCATATGTACCTATCCTTGGAACAATTCCGAACTGACAG
|||||  || || ||||||   | |  || ||| |||| |||   || || |  ||| |  |||||  |||||| | | ||| ||   ||||| || ||  | |||||| || | |  || |||||||||||||| || | ||||||| |||||||||| |  || |||||||| ||||| ||||||||||
gtaag--cttgtaatttcatttata--gaatcatgatcatttttcttaattccatca-taagcactatcttactatctatgccaaatacagAGGGAGTCTGAAAAGCCAAAGGTAGTGAAATGGTACTTCCCACAACTCAGGCTTGACCAACTCATATGCAGTTACCCTTGGAAAAATTCAGAACTGACAG
















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|211005146|gb|FL015709.1|FL015709
EST:     CTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTG                         AGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAG
genomic: CTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTGgtaagttctc ... ctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAG
EST: gi|71437996|gb|DR819046.1|DR819046
EST:     CTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTG                         AGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAG
genomic: CTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTGgtaagttctc ... ctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAG

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), 47 (downstream exon)
Score: 91

AAGGTTTTTTAAACATGTTGGAAGTATCTATCCTGGCAATGAGGCACCTACTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTGgtaagttctc ... ctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAGCTTGACAAACTCATATGTACCTATCCTTGGAACAATTCCGAACTGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

AAGGTTTTTTAAACATGTTGGAAGTATCTATCCTGGCAATGAGGCACCTACTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTGgtaagttctc ... ctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAGCTTGACAAACTCATATGTACCTATCCTTGGAACAATTCCGAACTGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

AAGGTTTTTTAAACATGTTGGAAGTATCTATCCTGGCAATGAGGCACCTACTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTGgtaagttctc ... ctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAGCTTGACAAACTCATATGTACCTATCCTTGGAACAATTCCGAACTGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 124

AAGGTTTTTTAAACATGTTGGAAGTATCTATCCTGGCAATGAGGCACCTACTGGTCTTTGTAGTGCGTACAAAAGTTTAAGTGAAGAAGATGTTGAAGTGgtaagttctc ... ctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAGCTTGACAAACTCATATGTACCTATCCTTGGAACAATTCCGAACTGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctttggttttatactgtcactgtgcactgccttactctgttgctaatagcagAGAGACTCCAAGAAGCCACAGATGGGAAAGTGGTACTTCCCACACCTAAAGCTTGACAAACTCATATGTACCTATCCTTGGAACAATTCCGAACTGACAG
                                           tgctaat  putative branch site (score: 124)
         ttttatact  TA-rich tract