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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtttaacaggacagtctgaatcacatagaaaattaatcagaatcggtgaatactgtatgcatttgttgttggttgctgatggaattaccttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGCTGCGTCAACACAGTGGGCTTCAATGAGGTCGGTGACACCCTCATATCGG

Basic information

species Zea mays
transcript GRMZM2G123709_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123709_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g39760.1 (Oryza sativa), 3'ss of exon 1
gtgtttaacaggacagtctgaatcacatagaaaattaatcagaatcggtgaatactgtatgcatttgttgttggttgctgatggaattaccttctt--tcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGCTGCGTCAACACAGTGGGCTTCAATGAGGTCGGTGACACCCTCATATCGG
||  |  || | ||||  |||     |       |||  ||  |||| | | || ||     | ||   |     |||| ||| ||||     | |   ||||| ||||||||||| || ||| ||||| |||||||  ||||||| || |||||||| ||||| || |||||||| | ||  || || |||||||||||||
gt-ctggactgaacagcttgatctgaactacctgtta-ccatgatcgttaactaatgggcagaattaaagaataatgctaatgtaattgttggcatgtacagGATCTTGTAATGCGCCTGCAGGTTCACAGGAAGCTCAACAGGCATACAGGCTGCGTGAACACGGTAGGCTTCAACGCGGATGGCGATACCCTCATATCGG
















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|149074562|gb|EE162962.2|EE162962
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|28909535|gb|CB330979.1|CB330979
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|89762910|gb|DY690325.1|DY690325
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGG
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGG
EST: gi|211523958|gb|FL270275.1|FL270275
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|211520963|gb|FL270268.1|FL270268
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|211523959|gb|FL270276.1|FL270276
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|76924931|gb|DV170201.1|DV170201
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|76934227|gb|DV173775.1|DV173775
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|148996165|gb|EE035435.2|EE035435
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|211523956|gb|FL270273.1|FL270273
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|76019007|gb|DT946177.1|DT946177
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|78111955|gb|DV530351.1|DV530351
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|148969559|gb|EE020388.2|EE020388
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|93014861|gb|EB640381.1|EB640381
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|211523955|gb|FL270272.1|FL270272
EST:     TCGGGGACCTCCTGCCTCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|149112432|gb|EE191333.2|EE191333
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|211523957|gb|FL270274.1|FL270274
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|76017451|gb|DT944621.1|DT944621
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|148940255|gb|EC885028.2|EC885028
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|78105452|gb|DV523870.1|DV523870
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|78086093|gb|DV514486.1|DV514486
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
EST: gi|148949179|gb|EC894616.2|EC894616
EST:     TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAG                         GACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC
genomic: TCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGC

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: 160

GTCCGCCGTCGCGGCGCGCCACGGCGCCGCGGACCTCTGCCTCCGCGAGGTCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGCTGCGTCAACACAGTGGGCTTCAATGAGGTCGGTGACACCCTCATATCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

GTCCGCCGTCGCGGCGCGCCACGGCGCCGCGGACCTCTGCCTCCGCGAGGTCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGCTGCGTCAACACAGTGGGCTTCAATGAGGTCGGTGACACCCTCATATCGG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 52

GTCCGCCGTCGCGGCGCGCCACGGCGCCGCGGACCTCTGCCTCCGCGAGGTCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGCTGCGTCAACACAGTGGGCTTCAATGAGGTCGGTGACACCCTCATATCGG


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 150

GTCCGCCGTCGCGGCGCGCCACGGCGCCGCGGACCTCTGCCTCCGCGAGGTCGGGGACCTCCTGCCGCGACGCTTCGCCCGCCGCGCGGCCGGTTCCGAGgtcagttccc ... cttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGCTGCGTCAACACAGTGGGCTTCAATGAGGTCGGTGACACCCTCATATCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtgaatactgtatgcatttgttgttggttgctgatggaattaccttctttcagGACCTTGTAATGCGGCTCCAGATTCACCGGAAGCTTGACAGGCACACGGGCTGCGTCAACACAGTGGGCTTCAATGAGGTCGGTGACACCCTCATATCGG
                              tgctgat  putative branch site (score: 150)
                                         ttaccttctttc  putative PPT
                 atttgtt  TA-rich tract