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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcgatcggcgccgcttaattccttcctaaagatctctagcttcttcttctagatgcggctcgatctgtgtggtgctggattgctgatgcgagtcgtctcgtggtcgtggccggccggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT

Basic information

species Zea mays
transcript GRMZM2G125850_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|211236186|gb|FL162466.1|FL162466
EST:     TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCC                         GTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
genomic: TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
EST: gi|37417331|gb|CF646318.1|CF646318
EST:     TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCC                         GTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
genomic: TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
EST: gi|24934556|gb|CA452774.1|CA452774
EST:     TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCC                         GTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
genomic: TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
EST: gi|50335221|gb|CO530347.1|CO530347
EST:     TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCC                         GTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
genomic: TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
EST: gi|89249586|gb|DY621372.1|DY621372
EST:     TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCC                         GTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC
genomic: TCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCC

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: 307

GTCCCTCGCCGCCGGCTCCGCCATCATGCTCGCGTCCTGGGCCACCAGGATCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 38

GTCCCTCGCCGCCGGCTCCGCCATCATGCTCGCGTCCTGGGCCACCAGGATCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT


Block sizes: 18 (upstream exon), 32 (downstream exon)
Score: 1

GTCCCTCGCCGCCGGCTCCGCCATCATGCTCGCGTCCTGGGCCACCAGGATCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GTCCCTCGCCGCCGGCTCCGCCATCATGCTCGCGTCCTGGGCCACCAGGATCGCCGAGGCGCCCCAGACGGACCTCGACTTCTGGAAGGCGCTCACTCCCgtgagtatcg ... ggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgctggattgctgatgcgagtcgtctcgtggtcgtggccggccggccgagcagGTTGCGATCGCGCACACGATCGGGCACGTCGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT
          tgctgat  putative branch site (score: 191)