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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtagccccatcatcggattcatccatccatcacatctgcttctgctgctgctgctgattctgtaattcaattcatacatcactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCCGGCCATCGCATCCGCCATGCCCAACCTCAGCCCCGGCCTCATCTTCATC

Basic information

species Zea mays
transcript GRMZM2G135044_T02
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|71298977|gb|DR785482.1|DR785482
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|211033315|gb|FL100502.1|FL100502
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTTCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|93282539|gb|EB674803.1|EB674803
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|88755773|gb|DY539914.1|DY539914
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|94472819|gb|EB701777.1|EB701777
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|50337658|gb|CO532784.1|CO532784
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|71426206|gb|DR807256.1|DR807256
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|211033314|gb|FL100501.1|FL100501
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTTCAAGCGCTGATGCTGCTGGGGATCAAGAAG
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAG
EST: gi|18169261|gb|BM339101.1|BM339101
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|78088288|gb|DV516681.1|DV516681
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|78121589|gb|DV539973.1|DV539973
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
EST: gi|93282784|gb|EB675048.1|EB675048
EST:     ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG                         GACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC
genomic: ACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCC

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: 34 (upstream exon), 49 (downstream exon)
Score: 28

GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCCGGCCATCGCATCCGCCATGCCCAACCTCAGCCCCGGCCTCATCTTCATC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 57

GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCCGGCCATCGCATCCGCCATGCCCAACCTCAGCCCCGGCCTCATCTTCATC


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 18

GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCCGGCCATCGCATCCGCCATGCCCAACCTCAGCCCCGGCCTCATCTTCATC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 18

GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGGgtacggtagc ... cactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCCGGCCATCGCATCCGCCATGCCCAACCTCAGCCCCGGCCTCATCTTCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgcttctgctgctgctgctgattctgtaattcaattcatacatcactcatcagGACAACCGCGTTCCAAGCGCTGATGCTGCTGGGGATCAAGAAGACCACGCCGGCCATCGCATCCGCCATGCCCAACCTCAGCCCCGGCCTCATCTTCATC
                 tgctgat  putative branch site (score: 18)
                            taattcaattcata  TA-rich tract