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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatatcagtccttatctctcaagcacaacataggattttgctattacctctttactcggatttggtgatgattcctgcattactgtagttataca...

Basic information

species Zea mays
transcript GRMZM2G138505_T01
intron # 10
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|9254423|gb|BE344891.1|BE344891
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|78081339|gb|DV509751.1|DV509751
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|211360336|gb|FL143959.1|FL143959
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|32864122|gb|CF003804.1|CF003804
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|101387921|gb|EB815974.1|EB815974
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|71762140|gb|DR960077.1|DR960077
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|211360335|gb|FL143958.1|FL143958
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|71772236|gb|DR970173.1|DR970173
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC

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: 45 (upstream exon), 47 (downstream exon)
Score: 117

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 100

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 107

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA