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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccacagctactacctgtgtgcttcgtaagacctatctatgcctgcacccaccagcacagggatatgtaccggcctgctcgtttcagctggaaca...

Basic information

species Zea mays
transcript GRMZM2G156218_T03
intron # 1
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|74234556|gb|DT642470.1|DT642470
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         ACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
EST: gi|71332306|gb|DR803091.1|DR803091
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         ACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
EST: gi|211539208|gb|FL281587.1|FL281587
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         ACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
EST: gi|71332305|gb|DR803090.1|DR803090
EST:     CCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         ACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
genomic: CCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
EST: gi|211539211|gb|FL281590.1|FL281590
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         ACACAAGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
EST: gi|74234555|gb|DT642469.1|DT642469
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         ACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
EST: gi|211539210|gb|FL281589.1|FL281589
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         ACACAAGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 16

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAGGCAGTCAATAGACTTCCGCCAGGAGCAGAGAATATACTTGGGATCTTTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 52

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAGGCAGTCAATAGACTTCCGCCAGGAGCAGAGAATATACTTGGGATCTTTG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 37

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAGGCAGTCAATAGACTTCCGCCAGGAGCAGAGAATATACTTGGGATCTTTG


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 35

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... gctactgcagACACAGGATCCAGTTGAAAACCAGAAGCTATGTGCCTATTTGGTTGAGAAGGCAGTCAATAGACTTCCGCCAGGAGCAGAGAATATACTTGGGATCTTTG