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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaatttctttttcatgctccctttgctctagttgtgctttctttaatggttctgttttaaacag

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 27
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 44
TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaatttctttttcatgctccctttgct--ctagttgtgctttctttaatggttctgttttaaacag
 || ||| |||| ||||||||||||||||||||||||||||||||||||||||| || ||  |||||||||| |||||||| ||||||||||||||| |||| |  |   ||| |||||||||||  |||  |  ||| |||| |||| | |||||||  |  ||  | |||
CACAGAGCTACTACTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGAAGTCAGCTACTCAAAGCTCTAAATGTCTTGATGCTTAAAATCTTGgtttgtat-cttcattttcatgctcagtttagttgctacttgttcttt-tctaatggtcatacttggagcag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 27
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 46
TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaatttcttttt-catgctccctttgctcta-gttgtgctttc-tttaatggttctgttttaaacag------------------------------------------------------------
||| ||| | ||||| |||||||| ||||| |||||||||| |||||||||||| ||||||||  | |||||  ||||||| ||||||||||| ||  ||||    || | | | | | |   | |||| |  | |  ||||  ||     || | |  | ||    |   ||                                                            
TACTGAGCTTCTTCTGTGGCTCTTGGATGATAGGGTTCCTCATATGGATGATGGAAGCCAATTGTTGAAAGCTTTAAATGTGTTGATGCTTAAGATTTTGgttaggaagtctttctctgccctccccctctattttctgttgaactgaaacttcaggcatttggcagatgtaggataatatggagaaaaacattatgatgcagctatttagtaactagtgtttgtcaatacag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 27
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 47
TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaattt--ctttttcatgctccctttgctctagttgtgctttctttaatggttc-tgttttaaacag--------------------------------------------
||| ||| | ||||| |||||||| ||||| |||||||||| |||||||||||| ||||||||  | |||||  ||||||| ||||||||||| || |||||    || | |  || | ||   |||||  | ||  ||   | |      |    |||  | |  | || |                                             
TACTGAGCTTCTTCTGTGGCTCTTGGATGATAGGGTTCCTCATATGGATGATGGAAGCCAATTGTTGAAAGCTTTAAATGTATTGATGCTTAAGATTCTGgttaggaactctgtctgtgtctctctccccctccttcaggcattcagcagatgtcagtttatatgctgaagaacattccggtgcagctattttagtaactagtgtttgtcaatacag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 27
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 5'ss of exon 46
TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaatttctttttcatgctccctttgctctagttgtgctttctttaatggttctgttttaaacag---------------------------
 || ||| |  | ||||||||  | |||||||| ||||| |  ||||| ||||| || ||| | || ||||| || ||||||||||||||||| ||||||||   || || |   || ||||||     |  ||    | ||      | ||    ||||  || |  |                            
AACAGAGCTCTTGCTTTGGCTTCTGGATGAAAGAGTTCCACGCATGGAAGATGGGAGTCAACTTCTTAAAGCTCTGAATGTTTTGATGCTTAAGATCCTGgt---cagatattcgttccatgctaaaggttttcatcatatgtggctatgaagttctctgacttcattatttttatttcttgttttatttaattcag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 27
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 16
TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaatttctttttcatgc-tccctttgctctagtt--gtgctttctttaatggttctgttttaaacag----------------
 || ||| |  | |||||||| || |||||||||||||||| ||||||||||||||||||| | || ||||| || ||||||||||||||||| |||||||| |      | |||   ||||  |   |||| | || ||   |  | ||| |  |    |  || | |  ||                
CACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTCATATGGATGATGGCAGCCAACTTCTGAAAGCTCTGAATGTTTTGATGCTTAAGATCCTGgt-taagttctacttcaacatgtataaatttgttgtattttcatagtatctgttctctcgccattctgactagtggcttacaaatgcag

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|194717113|gb|FK934266.1|FK934266
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGTTTAAAATCTTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|61118500|gb|DN559461.1|DN559461
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|87152573|gb|DY397362.1|DY397362
EST:     ATGGCAGCCAATTACTCAAAGCGCTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|32847226|gb|CD986907.1|CD986907
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|67035401|gb|CO463934.1|CO463934
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG

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: 208

TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 39

TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

TACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTCTTATGGATGATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG