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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccacatctccattgagccaaaaatattttacgtgtattttcatgtttccacacaagaacagaaaggggctaaaatatttttcctttttgtcag

Basic information

species Zea mays
transcript GRMZM2G443985_T04
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T04 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 5'ss of exon 10
GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccacatctccattgagccaaaaatattt-tacgtgt-attttcatgtttccacacaagaacagaaaggggctaaaatatttttcctttttgtcag-----------------------
||||||||||||| ||||||||||| || ||||| |||||||||  | ||||||||  |  |||  |||| |||| ||  | | ||||   || ||  ||  || ||   ||||||| | || | | |    ||   || ||                       
GTTTTATTGCACACTATGCTACTCTAGCCAGCAGAGACGTGgtatgttcacatctctgtcaagctgaaaacatttatatatatcatttctgtgattttactaaaaaa---aaaggggtttaattttctccaattgaggtgagaaactttttttatattttgtcag
















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|32938375|gb|CF043194.1|CF043194
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|6095550|gb|AW120217.1|AW120217
EST:     GGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|32938968|gb|CF043787.1|CF043787
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|488227|gb|T18808.1|T18808
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCG-A
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|32939806|gb|CF044625.1|CF044625
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTACTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|32939493|gb|CF044312.1|CF044312
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|76921243|gb|DV168509.1|DV168509
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|211132969|gb|FL170874.1|FL170874
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCATTCTA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTA

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: 41 (upstream exon), 49 (downstream exon)
Score: 230

GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 274

GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 303

GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 340

GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA