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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtccgtccgcctctacatcttcgatgtcgatcccaccggacctccgatgtttcgtgtgtttttgtctgattcggtcctccgctccctccttttctcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGCGACACGGCCACCTCCGCCCGGGTACAAAGGTACGAGGTCGCCGAAGCCA

Basic information

species Zea mays
transcript GRMZM2G017334_T01
intron # 1
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|76920924|gb|DV168378.1|DV168378
EST:     TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAG                         ATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGC
genomic: TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGC
EST: gi|31355922|gb|CD440279.1|CD440279
EST:     TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAG                         ATCAGCCGCAGGGTGTTCGATGTCATCCGGGGTGACCACCAGGGCCACGGC
genomic: TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGC
EST: gi|71444659|gb|DR825709.1|DR825709
EST:     TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAG                         ATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGC
genomic: TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGC
EST: gi|74245291|gb|DT653205.1|DT653205
EST:     TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAG                         ATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGC
genomic: TCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGC

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), 45 (downstream exon)
Score: 65

TGTGGTGGTTGACGAGAACGCCTCCTCCTTCCGATACACGCGCTCCCTCCTCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGCGACACGGCCACCTCCGCCCGGGTACAAAGGTACGAGGTCGCCGAAGCCA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 24

TGTGGTGGTTGACGAGAACGCCTCCTCCTTCCGATACACGCGCTCCCTCCTCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGCGACACGGCCACCTCCGCCCGGGTACAAAGGTACGAGGTCGCCGAAGCCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 21

TGTGGTGGTTGACGAGAACGCCTCCTCCTTCCGATACACGCGCTCCCTCCTCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGCGACACGGCCACCTCCGCCCGGGTACAAAGGTACGAGGTCGCCGAAGCCA


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 27

TGTGGTGGTTGACGAGAACGCCTCCTCCTTCCGATACACGCGCTCCCTCCTCCATAGCACCCTCCAGCTCATGGGATGCAAGCCACGCCACGCCTTCGAGgtccgtccgt ... tcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGCGACACGGCCACCTCCGCCCGGGTACAAAGGTACGAGGTCGCCGAAGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtgtgtttttgtctgattcggtcctccgctccctccttttctcttgtatagATCAGCCGCAGGGTGTTTGATGTCATCCGGGGTGACCACCAGGGCCACGGCGACACGGCCACCTCCGCCCGGGTACAAAGGTACGAGGTCGCCGAAGCCA
              gtctgat  putative branch site (score: 27)
               tctgattcggtcctcc  CT-rich tract
       tgttttt  TA-rich tract