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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTCTAGGAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatatgtcctttatttaatctgatattttcttccgttttgaggatttgctttatttatttgaacttgtattctaatgtgcag

Basic information

species Zea mays
transcript GRMZM2G098434_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098434_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g38930.1 (Oryza sativa), 5'ss of exon 2
ATTGTCTAGGAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatatgtcctttatttaatctgatattttcttccgttttgaggatttgctttat---ttatttgaact-tgtattctaatgtgcag
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ATTGTCTAGGCAGACGGTTAGGTCCACGGCTTCTTGGTAGGGGCAACGATGGCTCCATGgtactcacatctcctctgat-attacccttctcctttcaattttgtggatttgcttagttccttatttaatttctatattctaatgcgcag
















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|71436946|gb|DR817996.1|DR817996
EST:     GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATG                         AGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAA
genomic: GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAA
EST: gi|148947655|gb|EC893135.2|EC893135
EST:     GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATG                         AGGCTTGTGAGGGATTTATATGTGATGCTTG
genomic: GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTG
EST: gi|148966012|gb|EE016944.2|EE016944
EST:     AAGACGTTTAGGTCCGCGCCTTTCT-GGTAGGGGAAACGATGGTTCCATG                         AGGCTTGTGAGGGATTTATATGTGATGCTT
genomic: AAGACGTTTAGGTCCGCGCCTT-CTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTT
EST: gi|76286619|gb|DV026187.1|DV026187
EST:     GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATG                         AGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAA
genomic: GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAA
EST: gi|148956132|gb|EC901900.2|EC901900
EST:     GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATG                         AGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAA
genomic: GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAA
EST: gi|148995862|gb|EE035098.2|EE035098
EST:     AAGACGTTTAGGTCCGCGCCCTTCT-GGTAGGGGAAACGATGGTTCCATG                         AGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGA
genomic: AAGACGTTTAGGTCCGCGCC-TTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGA
EST: gi|148965944|gb|EE016860.2|EE016860
EST:     GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATG                         AGGCTTGTGAGGGATTTATATGTGATGC
genomic: GAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGC

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), 46 (downstream exon)
Score: 35

ATTGTCTAGGAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAAGCACCTCTTGACTTGAAGGTTCCAGAAACTTTTGATGAATTTATCTGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 72

ATTGTCTAGGAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAAGCACCTCTTGACTTGAAGGTTCCAGAAACTTTTGATGAATTTATCTGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 32

ATTGTCTAGGAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAAGCACCTCTTGACTTGAAGGTTCCAGAAACTTTTGATGAATTTATCTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 43

ATTGTCTAGGAAGACGTTTAGGTCCGCGCCTTCTTGGTAGGGGAAACGATGGTTCCATGgtacttatat ... taatgtgcagAGGCTTGTGAGGGATTTATATGTGATGCTTGATAAAGTAAATTCTGAGGAAGCACCTCTTGACTTGAAGGTTCCAGAAACTTTTGATGAATTTATCTGGG