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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCAAAATCCAGCAACTGGTGAGGTCCTGGCAAACGTGTCCTGTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaatgtttcagtgttcagtttttatgccttaatacctatattatattgtgttccagaatagagctgttgctgtcaaagtgttacaagattcta...

Basic information

species Zea mays
transcript GRMZM2G119482_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g07760.2 (Oryza sativa), 5'ss of exon 2
GTGCAAAATCCAGCAACTGGTGAGGTCCTGGCAAACGTGTCCTGTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaatgtttcag---tgttcagtttttatgccttaatacctatattatattgtgttccagaatagagctgttgctgtcaaagtgttacaagattcta
|| ||||||||||||||||| ||| || || || ||||||||||||||||||| ||||||||||||||| || ||||| |||||||||||||||||||||| |||| | || | | |||| ||||||||| | | | | || | || | | || | ||| | | | ||| |
GTTCAAAATCCAGCAACTGGAGAGACTCTTGCCAATGTGTCCTGTATGGGCAGCAAAGAAACATCTGATGCAATAGCTTCAGCTCACAGTACATTCTATTgtacgtcagaagtataaactacattcaatttttatgcttcagagttgctttagtaggcctgatctttttaatgttatt-tgattaaatttcttcgagaatt--
















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|76286306|gb|DV025874.1|DV025874
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT                         CTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|211223364|gb|FL262903.1|FL262903
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACAT-CTATT                         CTTGGAGTAAATTCACTGCAAGYGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|76289708|gb|DV029276.1|DV029276
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT                         CTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|149102730|gb|EE188270.2|EE188270
EST:     CAGCAAAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT                         CTTGGAGTAAACTCACTGCAAGTGAGAGGAGAAAGGCACTAA
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAA
EST: gi|211223367|gb|FL262906.1|FL262906
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATGCTATT                         CTTGGAGTAAATTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|211223366|gb|FL262905.1|FL262905
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACAT-CTATT                         CTTGGAGTAAATTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATGGT
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATGGT
EST: gi|211225422|gb|FL262911.1|FL262911
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACAT-CTATT                         CTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|76921995|gb|DV168797.1|DV168797
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCGCAGTACATTCTATT                         CTTGGAGTAAA
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAA
EST: gi|149000791|gb|EE038015.2|EE038015
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT                         CTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|78093012|gb|DV521386.1|DV521386
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT                         CTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|71330637|gb|DR802090.1|DR802090
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT                         CTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|211223365|gb|FL262904.1|FL262904
EST:     AGCAGACGAAACATCTGATGCTATTGCTTCTGCTCACAGTACAT-CTATT                         CTTGGAGTAAATTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
genomic: AGCAGA-GAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG
EST: gi|211223363|gb|FL262902.1|FL262902
EST:     CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT                         CTTGGAGTAAA
genomic: CAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 112

GTGCAAAATCCAGCAACTGGTGAGGTCCTGGCAAACGTGTCCTGTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

GTGCAAAATCCAGCAACTGGTGAGGTCCTGGCAAACGTGTCCTGTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 169

GTGCAAAATCCAGCAACTGGTGAGGTCCTGGCAAACGTGTCCTGTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 114

GTGCAAAATCCAGCAACTGGTGAGGTCCTGGCAAACGTGTCCTGTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATTgtaagtcaaa ... cttctcgcagCTTGGAGTAAACTCACTGCAAGTGAGAGGAGCAAGGCACTAAGAAAATG