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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgtctgcaggcttctgcgtagtttttttttttttttttttggggagggagggttcagatggaacaatgctcaaaatgcgattaatgtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGACAAGACGATTGTTCTACCTATGCCG

Basic information

species Zea mays
transcript GRMZM5G843914_T01
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|211540834|gb|FL337850.1|FL337850
EST:     AAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAG                         TGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGA
genomic: AAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAGgttggtgtct ... gtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGA
EST: gi|149090325|gb|EE179631.2|EE179631
EST:     AAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAG                         TGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGA
genomic: AAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAGgttggtgtct ... gtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGA
EST: gi|101392106|gb|EB817980.1|EB817980
EST:     AAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAG                         TGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGA
genomic: AAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAGgttggtgtct ... gtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGA

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: 140

GCGGCATGGAGGTGGAGGCTCTGGAGAAGAAGGGGCACGCAGCTTTTGCCAAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAGgttggtgtct ... gtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGACAAGACGATTGTTCTACCTATGCCG


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 49

GCGGCATGGAGGTGGAGGCTCTGGAGAAGAAGGGGCACGCAGCTTTTGCCAAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAGgttggtgtct ... gtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGACAAGACGATTGTTCTACCTATGCCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 38

GCGGCATGGAGGTGGAGGCTCTGGAGAAGAAGGGGCACGCAGCTTTTGCCAAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAGgttggtgtct ... gtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGACAAGACGATTGTTCTACCTATGCCG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 53

GCGGCATGGAGGTGGAGGCTCTGGAGAAGAAGGGGCACGCAGCTTTTGCCAAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATCCACGAGgttggtgtct ... gtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGACAAGACGATTGTTCTACCTATGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggagggagggttcagatggaacaatgctcaaaatgcgattaatgtttttccagTGGCAGATATTTTGAGGATATGTATGCTACAGACGCTTTGCGTTCTTCAGACAAGACGATTGTTCTACCTATGCCG
                                      gattaat  putative branch site (score: 53)
                                            tgtttttcc  CT-rich tract
                                       attaatgttttt  TA-rich tract