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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctttgtttcagaaccttcactatggtcctcaacattttctacacctttatttagaacattaagttgcatgccttattaatatatcactactatttttaatcatttccttgccctcatgtttgcttgacatagcttaataaattatgtccttactgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGTGGGGTACATCTGTGTCAGTAGTCGCCGTTACAAG

Basic information

species Zea mays
transcript GRMZM2G134770_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134770_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g41010.7 (Oryza sativa), 3'ss of exon 9
gtctttgtttcagaaccttcactatggtcctcaacattttctacacctttatttagaacat-------taagttgcatgccttattaatatatcactactatttttaatcatttccttgccctcatgtttgcttg-acatagcttaataaattatgtccttactgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGT--GGGGTACATCTGTGTCAGTAGTCGCCGTTACAAG
||   |  || ||||||| || |||| || |||  || | | |  ||||| |||||||||        ||| ||||||  |||||   | |   |  |  | |||   | |||| |||| | ||||  |  ||||  ||| |||| ||| || |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||  |||||  |||||||||||||||||| | |  |  
gtgcataatt-agaacctccagtatgatcatcattatatgccatgcctttctttagaacaattcaatataaattgcatatcttat--gttttctatcaacagtttcgtttatttgcttgtcttcatcatctcttgtgcatggcttgatatatcatgtccttactgttacagTGAGTCCTAGAACAGTTATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGTCTGGGGTCTATCTGTGTCAGTAGTCGCTGCTGTA--
















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|5005812|gb|AI711874.1|AI711874
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|71428348|gb|DR809398.1|DR809398
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|89248611|gb|DY620397.1|DY620397
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|6994049|gb|AW453263.1|AW453263
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|12970927|gb|BG267228.1|BG267228
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|32943442|gb|CF048261.1|CF048261
EST:     CATCACAGACGAACAATGCAAATGAATCNGAGGGAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|28910525|gb|CB331482.1|CB331482
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|94474683|gb|EB703641.1|EB703641
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|6952762|gb|AW424845.1|AW424845
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|78112738|gb|DV531132.1|DV531132
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|33097662|gb|CF057622.1|CF057622
EST:     GAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCGGCGTCGTCGTCAAG
genomic: GAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|76909152|gb|DV163248.1|DV163248
EST:     CTTCACAGGCGAACAATGCAAATGAATCAGCGGAAGATCGGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|211500849|gb|FL455460.1|FL455460
EST:     ATCACAGACGGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: ATCACAGAC-GAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|74243768|gb|DT651682.1|DT651682
EST:     CATCACAGCCGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|88752563|gb|DY536704.1|DY536704
EST:     CATCCCAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGGGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|211158909|gb|FK993540.1|FK993540
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCATCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|78026571|gb|DV494958.1|DV494958
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|31350190|gb|CD434547.1|CD434547
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCATCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|71762425|gb|DR960362.1|DR960362
EST:     TCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: TCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
EST: gi|89247194|gb|DY618980.1|DY618980
EST:     CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAG                         TGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG
genomic: CATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 79

CTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAAGCCATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGTGGGGTACATCTGTGTCAGTAGTCGCCGTTACAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 85

CTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAAGCCATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGTGGGGTACATCTGTGTCAGTAGTCGCCGTTACAAG


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

CTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAAGCCATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGTGGGGTACATCTGTGTCAGTAGTCGCCGTTACAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 60

CTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAAGCCATCACAGACGAACAATGCAAATGAATCAGCGGAAGATCAGGACAATCAGgtctttgttt ... actgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGTGGGGTACATCTGTGTCAGTAGTCGCCGTTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgccctcatgtttgcttgacatagcttaataaattatgtccttactgttacagTGAGTCCTAGAACAGTAATGAGGGTCAAGAAGGTCCAGCGTCGTCGTCAAGGTTCAGTCTGAATGTGGGGTACATCTGTGTCAGTAGTCGCCGTTACAAG
                                        tccttac  putative branch site (score: 60)
                                        tccttact  CT-rich tract
                      atagcttaataaatta  TA-rich tract