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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCAGTGCCGGCCTTCGCGCTGCTGCAGAGCAGGAAGAACACCCTCGCAGATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttcattccgaggctgtataaactattacatgcttctgattagtgattaatttggctatgcctgtacttagtaatcatcttcttaaatggttcaa...

Basic information

species Zea mays
transcript GRMZM2G409430_T02
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|18661883|gb|BM501632.1|BM501632
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|101391554|gb|EB817713.1|EB817713
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|71423081|gb|DR805945.1|DR805945
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|149010019|gb|EE041829.2|EE041829
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|101401938|gb|EB822595.1|EB822595
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|71449560|gb|DR830610.1|DR830610
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|149015081|gb|EE044836.2|EE044836
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|78113107|gb|DV531501.1|DV531501
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
EST: gi|18963165|gb|BM660276.1|BM660276
EST:     GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATG                         GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA
genomic: GATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAA

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: 89

GGTCAGTGCCGGCCTTCGCGCTGCTGCAGAGCAGGAAGAACACCCTCGCAGATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 24

GGTCAGTGCCGGCCTTCGCGCTGCTGCAGAGCAGGAAGAACACCCTCGCAGATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 10

GGTCAGTGCCGGCCTTCGCGCTGCTGCAGAGCAGGAAGAACACCCTCGCAGATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 39

GGTCAGTGCCGGCCTTCGCGCTGCTGCAGAGCAGGAAGAACACCCTCGCAGATGTTGCTACTATGTCGCACGTGCCCTCAGTCCCTGATCATGCAGAATGgtgaacttca ... gtttcattagGTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG