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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTAGCTATGAAGAAGGCAGAAGAATTTTCCTACTTCAGGCGGAGCAAGCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttccagccctcctacaatttatctgctgtccaattctgtaccattgttttataaagtttcttgtttcacaaaagaaaaccatgtctattcttaagttagctcatggtttttactacatactgctcttcag

Basic information

species Zea mays
transcript GRMZM2G102318_T01
intron # 3
splice site 5'
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|78118916|gb|DV537300.1|DV537300
EST:     GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTC                         TCTCCTGCCAAC
genomic: GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAAC
EST: gi|31354539|gb|CD438896.1|CD438896
EST:     GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTC                         TCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT
genomic: GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT
EST: gi|148973471|gb|EE024569.2|EE024569
EST:     GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTC                         TCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT
genomic: GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT
EST: gi|148962212|gb|EE013028.2|EE013028
EST:     GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTC                         TCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT
genomic: GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT
EST: gi|67030045|gb|CO458794.1|CO458794
EST:     GCTGAACGCCTTGTTCAATCTTTCAAGATAAATTACATCCCTGGCTTCTC                         TCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT
genomic: GCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGT

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: 44 (upstream exon), 49 (downstream exon)
Score: 35

GTGTTAGCTATGAAGAAGGCAGAAGAATTTTCCTACTTCAGGCGGAGCAAGCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGTGAAGACGATCCTGAGGGGCATAATAGAGAAGAGACAGAAGGCAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GTGTTAGCTATGAAGAAGGCAGAAGAATTTTCCTACTTCAGGCGGAGCAAGCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGTGAAGACGATCCTGAGGGGCATAATAGAGAAGAGACAGAAGGCAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

GTGTTAGCTATGAAGAAGGCAGAAGAATTTTCCTACTTCAGGCGGAGCAAGCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGTGAAGACGATCCTGAGGGGCATAATAGAGAAGAGACAGAAGGCAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GTGTTAGCTATGAAGAAGGCAGAAGAATTTTCCTACTTCAGGCGGAGCAAGCTGAACGCCTTGTTCAATCTTTCAAGACAAATTACATCCCTGGCTTCTCgtacggttcc ... tgctcttcagTCTCCTGCCAACAGAAAACAACAGAAGGATGAATGAAATCGACAGGGAGGTGAAGACGATCCTGAGGGGCATAATAGAGAAGAGACAGAAGGCAGCCAAG