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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgatagtttatctagcaatttctgcaattcaatagtatcagccaaagcagtcttcttttcatccatcccccagaaggccagaatgattatattttttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 13
gtatgttgatagtttatctagcaatttctgcaattcaatagtatcagccaaagcagtcttcttttcatccatcccccagaaggccagaatgattatatt-ttttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG
||||| |  | ||||| |    || || ||| | | |  ||    ||      ||  | ||| |   ||  |  ||||||| ||| || |  ||| ||| |||| |  ||||||||| ||||||||||||||||||| |||||||| |||||||| || || ||||||||||||||||| ||||| ||  | |  ||||||||||| || |
gtatgatact-gtttagcagcaaaattttgctaattaggag----aggattgacacccctctgtcattcgttagcccagaaagcctgagttgttaaattattttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTCGGTTATTCAGGCATTCAGTTTGATGCGGACCAGCTTGATATTTCCCTTG

upper sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 14
gtatgttgatagtttatctagcaatttctgcaattcaatagtatcagccaaagcagtcttctt--ttcatccatcccccagaaggccag--aatgattatattttttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG
                                     ||| | | | | |||| | |||| |   ||  || ||||  |  ||| | |   |   |   || | |||    ||||| ||||||| ||| |||||||| ||||||||||| ||||||    ||| |||||| || ||  ||  |||  |   | ||  ||||    |    ||||
--------------------------------gcatgataat-tgaactaaagaaatcttttacatttttcaatccggcttaagtctaattatccaacctaatgttt-catcagGCTGCTATATATGGTAGAGACCCCAATTGGGGACGCATTGCTGCTGCAGCTGGTTACTCGGGGGTTTCATTCCATCAAGATTTACTTAGGGTAGAGCTGG
















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|32934567|gb|CF039379.1|CF039379
EST:     CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
genomic: CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
EST: gi|22552553|gb|BU102392.1|BU102392
EST:     TGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
genomic: TGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
EST: gi|32835096|gb|CD974774.1|CD974774
EST:     CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
genomic: CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
EST: gi|20802518|gb|BQ293568.1|BQ293568
EST:     CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
genomic: CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
EST: gi|32928445|gb|CF033257.1|CF033257
EST:     CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGAACGAATTGCTTGCTCAGTT
genomic: CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
EST: gi|166482515|gb|EG042058.1|EG042058
EST:     CTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
genomic: CTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
EST: gi|78543892|gb|DV621390.1|DV621390
EST:     CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
genomic: CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
EST: gi|32833027|gb|CD972705.1|CD972705
EST:     CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTG
genomic: CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTG
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA                         GCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT
genomic: CAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTT

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), 48 (downstream exon)
Score: 149

GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgat ... tttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttcttttcatccatcccccagaaggccagaatgattatattttttgtgacagGCCGCTATATTTGGAAGAGACCCAAATTGGGGACGAATTGCTTGCTCAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGG
                                        tatttttt  CT-rich tract
                              agaatgattatatttt  TA-rich tract