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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttatattctcattagctgcagcttccattaataaatggtcttccttaacctatcttcttgtttctttttggag

Basic information

species Zea mays
transcript GRMZM2G082099_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082099_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 9
CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttatattctcat--tagctgc-agcttccattaata-aatggtcttccttaacctatcttcttgtttctttttggag
|||| || ||||| |||      || || |||||||||||||| ||| |||||||||||||||||||||  ||||||||    || |||| | ||  |  | ||| | || | ||   | |  | | |  | |||| ||||  |  
CATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAGgttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttcag--
















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|61118494|gb|DN559455.1|DN559455
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
EST: gi|32928776|gb|CF033588.1|CF033588
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
EST: gi|61118493|gb|DN559454.1|DN559454
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
EST: gi|32934388|gb|CF039200.1|CF039200
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACCAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTA
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAA-CAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTA
EST: gi|28390302|gb|CB250149.1|CB250149
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGG

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: 587

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCAATGGCATACACCCTTATTTTCCTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCAATGGCATACACCCTTATTTTCCTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCAATGGCATACACCCTTATTTTCCTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggttata ... ctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCAATGGCATACACCCTTATTTTCCTGATA