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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcttagaaattagcacttctatctaaggttgggtgttaggtgttgtggtattcaatattagtatttttttattcttatggtggtgttttgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATAGGGAATTTAGCTAGAGGTTTAAGAGCCCATTTTTCTGGAAATGCCCGAA

Basic information

species Zea mays
transcript GRMZM2G070126_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070126_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------------tggcttagaaattagcacttctatctaaggttgg-gtgttaggtgttgtggtattc--------aatattagtatttttttattcttatggtggtgttttgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATAGGGAATTTAGCTAGAGGTTTAAGAGCCCATTTTTCTGGAAATGCCCGAA
                                                              | | ||  |  ||    |   | |  || ||     ||||   | || |  |||          ||||| | |   || |   |    |  | || |||  |  | ||||| || || ||||| |||||||||||||| |||||||||||||| |||||||| |||||||||| |||||||||| | ||||||||||||||| | ||  
gttaatattctgctccaagtctctatgtattttgtacattcaaatttgcagtcatgtttagtttggttttatgttgtttcgagtgttcaaagtgaacatgtttttttttctaatatatgtttgtgaaatatgattcacttgtatctgccctttttgtttttgttattacagCTTATTACCGATGTCAATTTGGCTGTTTCAGTGGAAGCTACTCAAGCAATAGGAAATTTAGCTAAAGGTTTAAGAACTCATTTTTCTGGAAATTCACGGG
















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|166681096|gb|EG058281.1|EG058281
EST:     TGAAATTTGCCGGACACTAAAGAAG                         CTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATA
genomic: TGAAATTTGCCGGACACTAAAGAAGgtcaagtctc ... tgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATA
EST: gi|211274055|gb|FL438415.1|FL438415
EST:     NNNNNNTTGCTCCTGGTGATTTTCATGAAATTTGCCGGACACTAAAGAAG                         CTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATA
genomic: AAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCCGGACACTAAAGAAGgtcaagtctc ... tgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATA

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: 196

GTCAGAGAGAAGGGATGCTGTGGCAGAGCTAACCAAGCTTGCGTCAGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCCGGACACTAAAGAAGgtcaagtctc ... tgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATAGGGAATTTAGCTAGAGGTTTAAGAGCCCATTTTTCTGGAAATGCCCGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

GTCAGAGAGAAGGGATGCTGTGGCAGAGCTAACCAAGCTTGCGTCAGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCCGGACACTAAAGAAGgtcaagtctc ... tgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATAGGGAATTTAGCTAGAGGTTTAAGAGCCCATTTTTCTGGAAATGCCCGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 31

GTCAGAGAGAAGGGATGCTGTGGCAGAGCTAACCAAGCTTGCGTCAGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCCGGACACTAAAGAAGgtcaagtctc ... tgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATAGGGAATTTAGCTAGAGGTTTAAGAGCCCATTTTTCTGGAAATGCCCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GTCAGAGAGAAGGGATGCTGTGGCAGAGCTAACCAAGCTTGCGTCAGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCCGGACACTAAAGAAGgtcaagtctc ... tgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATAGGGAATTTAGCTAGAGGTTTAAGAGCCCATTTTTCTGGAAATGCCCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggtattcaatattagtatttttttattcttatggtggtgttttgtgctgcagCTCATCACAGATGTTAATTTGGCTGTTTCGGTGGAAGCTACTCAGGCAATAGGGAATTTAGCTAGAGGTTTAAGAGCCCATTTTTCTGGAAATGCCCGAA
     tattcaatattagtat  TA-rich tract