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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCATGGCGAGCCTGTCGTCGCCGAGTCTCCTCTCTTCCTTCCTCGGCGACCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgcccgccccatcttccgcactgctccgcggttgtgcccctggtttcatctcgtcggcccagagcagagttcgctgagatggctcttccttgcag

Basic information

species Zea mays
transcript GRMZM2G101438_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 1
CCCATGGCGAGCCTGTCGTCGCCGAGTCTCCTCTCTTCCTTCCTCGGCGACCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgcccgccccatcttc----cgcactgctccgcg---gttgtgccc-ctggtttcatctcgtcggcccagagcagagttcgctgagatggctc-ttccttgcag---------------------------------------------------
|||||||||| |  |||||||||| | || ||||| |||||||||||||||||||||     | |||        |  || ||||||   || |  |||||||   ||||  |||   |||    | | |  |||||||   |  | || | ||   | || |||| ||   |    | |  | |||||     || | ||    || |                                                   
CCCATGGCGACCTCGTCGTCGCCGCGCCTGCTCTCCTCCTTCCTCGGCGACCGCCTCCTCTCCGCCAGCGCCAGGCCGCTCCTCCGCGGGGCCGCTCCAGgtaggcgcccttcccccattcttctctcgcaactccgcgcgcgcggcgcgcactccctccacctcg-cgaatcgcgactgcctccgctgccccagcgcgttagcggcgggcaagagtttactgaggctgctccggctccgggtgggctctctttttgcag
















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|78075681|gb|DV504115.1|DV504115
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
EST: gi|101399011|gb|EB821378.1|EB821378
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
EST: gi|76912468|gb|DV164746.1|DV164746
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
EST: gi|211227812|gb|FL170955.1|FL170955
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
EST: gi|211227811|gb|FL170954.1|FL170954
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
EST: gi|71436246|gb|DR817296.1|DR817296
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
EST: gi|148995508|gb|EE034697.2|EE034697
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
EST: gi|78082005|gb|DV510417.1|DV510417
EST:     CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAG                         GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG
genomic: CCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGG

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: 46 (upstream exon), 48 (downstream exon)
Score: 23

CCCATGGCGAGCCTGTCGTCGCCGAGTCTCCTCTCTTCCTTCCTCGGCGACCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGGATATCCTATTTAACAGGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 42

CCCATGGCGAGCCTGTCGTCGCCGAGTCTCCTCTCTTCCTTCCTCGGCGACCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGGATATCCTATTTAACAGGAG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 25

CCCATGGCGAGCCTGTCGTCGCCGAGTCTCCTCTCTTCCTTCCTCGGCGACCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGGATATCCTATTTAACAGGAG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 6

CCCATGGCGAGCCTGTCGTCGCCGAGTCTCCTCTCTTCCTTCCTCGGCGACCGCCTCGCACTCTCCACTAGGCCTCTCCTTCTCCGCTCCGCTGTCCCAGgtacctgccc ... ttccttgcagGCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGGATATCCTATTTAACAGGAG