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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtattatagatcaagctcttttgatatttttcacataccatacctaaatatcggatgcattacctaatataccaatttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATTGTCATGCATTAAACACATCAAAACAGTCCATGGGGCAATACTCAGGCTC

Basic information

species Zea mays
transcript GRMZM2G074436_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074436_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g41990.1 (Oryza sativa), 3'ss of exon 4
gtgtgtattatagatcaagctcttttgatatttttcacataccatacctaaatat-cggatgcattacctaatataccaatttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATTGTCATGCATTAAACACATCAAAACAGTCCATGGGGCAATACTCAGGCTC
|||||||  | | |   | || ||| ||| | |||  | |    |    ||| |  | |||||||||| | ||||| |||  |  |||||||||||| | || ||||||||||| ||  |||| ||||||||||| |||||||||||  | ||||||||||| || ||  |||||||| | || |||||
gtgtgtacgacaaacagaactattt-gatctcttttgcctgttgtgttaaaaaagactgatgcattacttgatatatcaacgt--gcagGCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATTGTCATGCGCTGAACACATCAAAGCAATCTTTGGGGCAACATTCTGGCTC
















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|149084451|gb|EE173909.2|EE173909
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|110516560|gb|EE021147.1|EE021147
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|211419602|gb|FL445134.1|FL445134
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGGAGCTGCCATATGCATAACG                         GCTTGTCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCACATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|91053444|gb|EB163862.1|EB163862
EST:     CCCATCCCAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTATTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|60358147|gb|DN225120.1|DN225120
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|211512285|gb|FL437428.1|FL437428
EST:     CATCACAGTCGTATGCTTTGATATGTGGGAGCTGCCATATGCATAACG                         GCTTGTCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCACATT
genomic: CATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|60356654|gb|DN223627.1|DN223627
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|71759878|gb|DR957815.1|DR957815
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|71427127|gb|DR808177.1|DR808177
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|110537981|gb|EE042009.1|EE042009
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|94476106|gb|EB705064.1|EB705064
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTATTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|78115257|gb|DV533645.1|DV533645
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|71431982|gb|DR813032.1|DR813032
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|60338299|gb|DN205272.1|DN205272
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|74239242|gb|DT647156.1|DT647156
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|211218961|gb|FL467829.1|FL467829
EST:     CAGTCGTATGCTTTGATATGTGGGAGCTGCCATATGCATAACG                         GCTTGTCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCACATT
genomic: CAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|101397835|gb|EB820794.1|EB820794
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTATTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|211175270|gb|FL438825.1|FL438825
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGGAGCTGCCATATGCATAACG                         GCTTGTCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCACATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|101399967|gb|EB821830.1|EB821830
EST:     CCCATCCCAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTATTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|78120900|gb|DV539284.1|DV539284
EST:     TGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: TGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|16918238|gb|BM073650.1|BM073650
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|78115258|gb|DV533646.1|DV533646
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCCGAAAG-AAGATTACCCACATGTTACTTACTACT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCC-GAAAGGAAGATTACCCACATGTTACTTACTACT
EST: gi|78091241|gb|DV519615.1|DV519615
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|76933106|gb|DV173323.1|DV173323
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTATTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|71436210|gb|DR817260.1|DR817260
EST:     TGGCAGTTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTATTATTGCCCGCTTT
genomic: TGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
EST: gi|60356656|gb|DN223629.1|DN223629
EST:     CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACG                         GCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT
genomic: CCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATT

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: 48 (upstream exon), 48 (downstream exon)
Score: 43

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGGGGAGGACCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATTGTCATGCATTAAACACATCAAAACAGTCCATGGGGCAATACTCAGGCTC


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

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGGGGAGGACCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATTGTCATGCATTAAACACATCAAAACAGTCCATGGGGCAATACTCAGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGGGGAGGACCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATTGTCATGCATTAAACACATCAAAACAGTCCATGGGGCAATACTCAGGCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 63

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGGGGAGGACCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtatta ... atttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATTGTCATGCATTAAACACATCAAAACAGTCCATGGGGCAATACTCAGGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacataccatacctaaatatcggatgcattacctaatataccaatttttgcagGCTTGGCCCGAAAGGAAGATTACCCACATGTTACTTACTACTGCCCGCATTGTCATGCATTAAACACATCAAAACAGTCCATGGGGCAATACTCAGGCTC
                                acctaat  putative branch site (score: 63)
                                              tttttgc  putative PPT
                                   taatataccaattttt  TA-rich tract