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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggtcacaaatttatacttgccatgttcttttttggaaaccagttaatagaatgtcacgatagttgaatagtgttgctttcag

Basic information

species Zea mays
transcript GRMZM2G023528_T05
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 5'ss of exon 3
TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggtcacaaatttatacttgccatgttcttttttggaaaccagttaatagaatgtcacgatagttgaatagtgttgctttcag
|| |||||||||||||| || || ||    |||| ||||||||||||||| |||||||| |||||||| || || ||||| |||||||||  ||| | ||||    |    ||    | |||||| || | || || || ||  ||  |      ||                    
TTTCCTGCACTTCGAGAATTTGTTGGTACAGGAAGGCCTGTCTGGGGAACTTGTGCTGGACTCATCTTCCTAGCTAACAAGGCAGTAGgtatgtgagccacagcaattggtttaatct-ttctttctttggaatcaattgatgaaagttatttgcag--------------------
















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|50327771|gb|CO522897.1|CO522897
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|6020368|gb|AW065296.1|AW065296
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|71318383|gb|DR795955.1|DR795955
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|5895630|gb|AW036876.1|AW036876
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|33467208|gb|CF244257.1|CF244257
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|74233030|gb|DT640944.1|DT640944
EST:     GGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: GGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|40303169|gb|CK347556.1|CK347556
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC

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: 47

TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG