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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGGTCTTATCTATGTTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgcatgacctcaatcaattggcaagcatgtactcttcgtctgaagttgcattacatttgtatatatctaatttcttatgcaaactcag

Basic information

species Zea mays
transcript GRMZM2G072865_T05
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G072865_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 2
GTAGGTCTTATCTATGTTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgcatgacctcaatcaattggcaagcatgtactcttcgtctgaagttgcattacatttgtatata-tctaatttcttatgcaaactcag
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GTGGCTCTTATTTATGTTGTATTAATTGCTGTAGTTCTGCAGCGATTGCCAATAAGCTTTTCTCAGgtactgatgaatgcacttcattactt--caatcaactaatgaacatactcggttatatctttaatagatataatatagtttcttgtgtata-tcag
















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|32926564|gb|CF031376.1|CF031376
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32925973|gb|CF030785.1|CF030785
EST:     TTGTATTGATTGCGGTAGTTTTACAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32925914|gb|CF030726.1|CF030726
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGGGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32926844|gb|CF031656.1|CF031656
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32929777|gb|CF034589.1|CF034589
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32924793|gb|CF029605.1|CF029605
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32926859|gb|CF031671.1|CF031671
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32926579|gb|CF031391.1|CF031391
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32925296|gb|CF030108.1|CF030108
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA

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: 47 (upstream exon), 47 (downstream exon)
Score: 34

GTAGGTCTTATCTATGTTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 29

GTAGGTCTTATCTATGTTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 28

GTAGGTCTTATCTATGTTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 40

GTAGGTCTTATCTATGTTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG