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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcatgatttcttaatcagcagataggtttctattgtaggcatatgtctttcctttttgagtaacatttgccatcattattgctcgcagGTCTTTGCTGTGGATATACATCCAG

Basic information

species Zea mays
transcript GRMZM2G048740_T03
intron # 4
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|71320313|gb|DR796903.1|DR796903
EST:     ACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAG                         GTCTTTGCTGTGGATATACATCCAG
genomic: ACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAGgtgaagcatg ... ttgctcgcagGTCTTTGCTGTGGATATACATCCAG
EST: gi|149078416|gb|EE167191.2|EE167191
EST:     ACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAG                         GTCTTTGCTGTGGATATACATCCAGCTGCCA
genomic: ACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAGgtgaagcatg ... ttgctcgcagGTCTTTGCTGTGGATATACATCCAGCTGCCA
EST: gi|71434262|gb|DR815312.1|DR815312
EST:     CAGGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCCGTATTAGTGAG                         GTCTTTGCTGGGGATATACATCCAGCTGC
genomic: CAGGG-ACGCAAAGTTTTGGCATTGGCACTGCAAAGCC-GTATTAGTGAGgtgaagcatg ... ttgctcgcagGTCTTTGCTGTGGATATACATCCAGCTGC

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: 43 (upstream exon), 25 (downstream exon)
Score: 41

GGCTACCAATCGTTGCAATCATACAGGATAGCCAATATATTATGGAACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAGgtgaagcatg ... ttgctcgcagGTCTTTGCTGTGGATATACATCCAG


Block sizes: 48 (upstream exon), 25 (downstream exon)
Score: 53

GGCTACCAATCGTTGCAATCATACAGGATAGCCAATATATTATGGAACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAGgtgaagcatg ... ttgctcgcagGTCTTTGCTGTGGATATACATCCAG


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 70

GGCTACCAATCGTTGCAATCATACAGGATAGCCAATATATTATGGAACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAGgtgaagcatg ... ttgctcgcagGTCTTTGCTGTGGATATACATCCAG


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 60

GGCTACCAATCGTTGCAATCATACAGGATAGCCAATATATTATGGAACCAGGGACGCAAAGTTTTGGCATTGGCACTGCAAAGCCGTATTAGTGAGgtgaagcatg ... ttgctcgcagGTCTTTGCTGTGGATATACATCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaggcatatgtctttcctttttgagtaacatttgccatcattattgctcgcagGTCTTTGCTGTGGATATACATCCAG
                        gagtaac  putative branch site (score: 60)
 atcattatt  TA-rich tract