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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtacgttcccgggccgcggcgagccggccggcgaccggcggtgctgcggacgatgcctttctttcactgataatcatctgccgccatcgttctggtcccgacacgtgcccttgcttcccgttctgctcccggcacttaacttggtcgcatatactattcctgtaacctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGG

Basic information

species Zea mays
transcript GRMZM2G000158_T01
intron # 2
splice site 3'
intron type U2

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|22490343|gb|BU050266.1|BU050266
EST:     GGAGCTGCTCCGCACGCTCGAGCGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTTGCCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|18964862|gb|BM661253.1|BM661253
EST:     GGAGCTGCTCCGCACGCTCGAGCGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTTGCCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|18963969|gb|BM660732.1|BM660732
EST:     GGAGCTGCTCCGCACGCTCGAGCGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAG
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAG
EST: gi|87151978|gb|DY396767.1|DY396767
EST:     GGAGCTGCTCCGCACGCTCGAGCGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTTGCCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|74234745|gb|DT642659.1|DT642659
EST:     GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAG                         A--A-G-A-----CGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|71762442|gb|DR960379.1|DR960379
EST:     GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|14243352|gb|BG841066.2|BG841066
EST:     GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|60350945|gb|DN217918.1|DN217918
EST:     GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAA-C--C-A-                         A-CA---AGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|71448007|gb|DR829057.1|DR829057
EST:     GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|87151801|gb|DY396590.1|DY396590
EST:     GGAGCTGCTCCGCACGCTCGAGCGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTTGCCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
EST: gi|78081855|gb|DV510267.1|DV510267
EST:     GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAG                         ATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC
genomic: GGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATC

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: 45 (upstream exon), 46 (downstream exon)
Score: 6

GGGGTGCCCATCGGGCGGAAGGTGGACGTGTCCATCCACGGCTCGTACCAGGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 5

GGGGTGCCCATCGGGCGGAAGGTGGACGTGTCCATCCACGGCTCGTACCAGGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGG


Block sizes: 46 (upstream exon), 20 (downstream exon)
Score: 2

GGGGTGCCCATCGGGCGGAAGGTGGACGTGTCCATCCACGGCTCGTACCAGGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 55

GGGGTGCCCATCGGGCGGAAGGTGGACGTGTCCATCCACGGCTCGTACCAGGAGCTGCTCCGCACGCTCGAGAGCATGTTCCCTTCGGGTAACCAACAAGgtgcgtacgt ... cctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgctcccggcacttaacttggtcgcatatactattcctgtaacctctggcagATCATGCAGAAGACGAGGTGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGG
                                       ctgtaac  putative branch site (score: 55)
                                             cctct  CT-rich tract
                            atatactatt  TA-rich tract