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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgccagcattttaataccattgttgttccagcagtgtttgacttctgatactaactagctacttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGGTTCGGAAACCATTACCCCAAGCATGTTCACCACCGGGGCGCCTCGATCC

Basic information

species Zea mays
transcript GRMZM2G003379_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003379_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g21210.1 (Oryza sativa), 3'ss of exon 5
gtatgctgccagcattttaat------accattgttgttccagcagtgtttgacttctgatactaactagctacttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGGTTCGGAAACCATTACCCCAAGCATGTTCACCACCGGGGCGCCTCGATCC
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gtaggtttgcagagtttaaaatgttggaatcttgtaattccagcagtttttaactcctgatactaattcactacttatttcagATCGAATACATCTTAGGAAAAAATCCTTTGAAGATGAGCTATGTGGTTGGTTACGGAAACCGTTACCCTAAACGTGTTCATCATCGGGGTGCCTCGATCC
















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|148996357|gb|EE035644.2|EE035644
EST:     GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAG                         ATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
genomic: GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
EST: gi|110964561|gb|EE184461.1|EE184461
EST:     GCCCACATTTTTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAG                         ATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
genomic: GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
EST: gi|74241493|gb|DT649407.1|DT649407
EST:     GCCCACATTTTTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAG                         ATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
genomic: GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
EST: gi|60351728|gb|DN218701.1|DN218701
EST:     GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAG                         ATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
genomic: GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
EST: gi|211082914|gb|FL076243.1|FL076243
EST:     GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAG                         ATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
genomic: GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
EST: gi|148937056|gb|EC881230.2|EC881230
EST:     AGTTTTGCAAGGACTCAG                         ATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
genomic: AGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
EST: gi|71308746|gb|DR790610.1|DR790610
EST:     GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAG                         ATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG
genomic: GCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGG

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 3 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 19

TGTGTTCAGTGACTATCTTGAGGCTGCGGATACTCCTGGGTGGTATTGTGGCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGGTTCGGAAACCATTACCCCAAGCATGTTCACCACCGGGGCGCCTCGATCC


Block sizes: 30 (upstream exon), 30 (downstream exon)
Score: 2

TGTGTTCAGTGACTATCTTGAGGCTGCGGATACTCCTGGGTGGTATTGTGGCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGGTTCGGAAACCATTACCCCAAGCATGTTCACCACCGGGGCGCCTCGATCC


Block sizes: 41 (upstream exon), 9 (downstream exon)
Score: 2

TGTGTTCAGTGACTATCTTGAGGCTGCGGATACTCCTGGGTGGTATTGTGGCCCACATTTCTACTCTATCGAGGTTCTCCGCAGTTTTGCAAGGACTCAGgtatgctgcc ... cttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGGTTCGGAAACCATTACCCCAAGCATGTTCACCACCGGGGCGCCTCGATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattgttgttccagcagtgtttgacttctgatactaactagctacttccatcagATCGAGTACATCTTAGGGAAAAATCCATTGAAGATGAGCTATGTGGTTGGGTTCGGAAACCATTACCCCAAGCATGTTCACCACCGGGGCGCCTCGATCC
                                tactaac  putative branch site (score: 2)
                                          ctacttcc  putative PPT
                               atactaa  TA-rich tract