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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCAGCGAAGTTTTTGTGCATCAAATGATACATTCCATTGAGTTTGTACTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctcttgtgatttgtgatgttttgttggttgctgccagttttaactttgcccgtttcaacccctcacttctgtgtattgattgttggtttcag

Basic information

species Zea mays
transcript GRMZM5G801793_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801793_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g61780.1 (Oryza sativa), 5'ss of exon 16
ATTTCAGCGAAGTTTTTGTGCATCAAATGATACATTCCATTGAGTTTGTACTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctcttgtgatttgtgatgttttgttggttgctgccagttttaactttgcccgtttcaacccctcacttctgtgtattgattgttggtttcag
| || || ||||||||||||||||||||||||||||||||||| ||||||||||| || || || ||||||||||| |||||||| ||||||||  | |||||||| | ||   ||||    |||| | |||  | ||  ||  | |     ||| | |   ||    |||  ||| | | | |  | ||   |||||
ACTTTAGTGAAGTTTTTGTGCATCAAATGATACATTCCATTGAATTTGTACTTGGCGCTGTCTCCAATACTGCATCGTATCTTCGGCTTTGGGCATTAAGgtttgcttttt---attt----tgttatattgcatactttcatatctgtaggtgctcttcataaatt-tcatgtctttctttcg--tcttatattcag
















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|18661093|gb|BM501206.1|BM501206
EST:     CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAG                         CTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
genomic: CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
EST: gi|211504649|gb|FL183082.1|FL183082
EST:     CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAG                         CTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
genomic: CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
EST: gi|24934155|gb|CA452373.1|CA452373
EST:     CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAG                         CTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
genomic: CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
EST: gi|32940571|gb|CF045390.1|CF045390
EST:     CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAG                         CTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
genomic: CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
EST: gi|6227219|gb|AW155818.1|AW155818
EST:     CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAG                         CTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
genomic: CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
EST: gi|33091106|gb|CF051100.1|CF051100
EST:     CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAG                         CTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT
genomic: CTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACT

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: 46 (upstream exon), 44 (downstream exon)
Score: 39

ATTTCAGCGAAGTTTTTGTGCATCAAATGATACATTCCATTGAGTTTGTACTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACTTGCCTGGGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 78

ATTTCAGCGAAGTTTTTGTGCATCAAATGATACATTCCATTGAGTTTGTACTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACTTGCCTGGGG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 115

ATTTCAGCGAAGTTTTTGTGCATCAAATGATACATTCCATTGAGTTTGTACTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACTTGCCTGGGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 64

ATTTCAGCGAAGTTTTTGTGCATCAAATGATACATTCCATTGAGTTTGTACTTGGTGCAGTTTCAAATACTGCATCTTATCTTCGACTTTGGGCTCTGAGgtttgcctct ... ttggtttcagCTTGGCGCATTCAGAGCTGTCAACAGTTTTCTATGAGAAGTTGCTGTTACTTGCCTGGGG