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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttatttgttgttgccgattgccctcatcattagttcattacgaagacatgtcaaaagcagaacacttgctcatgtctttttatgcacattatgttgattttctaatttctaaaatcccatggtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG

Basic information

species Zea mays
transcript GRMZM2G115518_T01
intron # 8
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|110537607|gb|EE041667.1|EE041667
EST:     AGCTGCTTGACCCCAGAGATGGGTTGGTGTCACTCGACAACTTTCGGGCG                         GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
EST: gi|67016487|gb|CO445236.1|CO445236
EST:     AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGACG                         GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
EST: gi|76284391|gb|DV023959.1|DV023959
EST:     AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCG                         GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
EST: gi|110527857|gb|EE032041.1|EE032041
EST:     AGCTGCTTGAACCCAGAGATGGGTTTGTGTCACTCGACAACTTTCGGGCG                         GCTTTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
EST: gi|211096943|gb|FL476438.1|FL476438
EST:     AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGACG                         GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
EST: gi|31357313|gb|CD441670.1|CD441670
EST:     AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCG                         GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
EST: gi|78104805|gb|DV523223.1|DV523223
EST:     AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGACG                         GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
EST: gi|6626368|gb|AW257900.1|AW257900
EST:     AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGACG                         GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAG

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), 46 (downstream exon)
Score: 58

ATCTAAGGCTTTAAGCGAGGATGAACTTTTGTATCTTAGGTTGCAGTTTAAGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

ATCTAAGGCTTTAAGCGAGGATGAACTTTTGTATCTTAGGTTGCAGTTTAAGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

ATCTAAGGCTTTAAGCGAGGATGAACTTTTGTATCTTAGGTTGCAGTTTAAGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

ATCTAAGGCTTTAAGCGAGGATGAACTTTTGTATCTTAGGTTGCAGTTTAAGCTGCTTGAACCCAGAGATGGGTTCGTGTCACTCGACAACTTTCGGGCGgtgcgttatt ... gtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatgcacattatgttgattttctaatttctaaaatcccatggtgtaaccagGCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG
                              ttctaaa  putative branch site (score: 123)
           attatgttgattttct  TA-rich tract