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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaatgtaccttgattcttttgtagtttgctatgcatcagcagcatttaatagcatgataataacattctctgtactaacagcacatgtggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT

Basic information

species Zea mays
transcript GRMZM2G085474_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------gaaaatgtaccttgattctttt-gtagtttgctatgcatcagcagcatttaata--gcatgataataacat-------tctctgtactaacagcacatgtggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT
                                                              |||| || |  |   |||  ||     ||||  || |    |||   |||| |   ||   ||| | |  |        ||   ||||        || ||    || ||||||| |||||||| |||||||||||||||||| |||| ||||||||||| ||||| |||||||| |||||||||||||| ||||||
gtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT
















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|16919248|gb|BM074105.1|BM074105
EST:     CGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCA                         GAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG
genomic: CGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG
EST: gi|71448616|gb|DR829666.1|DR829666
EST:     CATTTTCTGCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCA                         GAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG
genomic: CATTTTCTGCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG
EST: gi|89106387|gb|DY576604.1|DY576604
EST:     GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCA                         GAAAAGATTAATGTCCATGGAGG
genomic: GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGG
EST: gi|6526946|gb|AW216191.1|AW216191
EST:     GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCA                         GAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG
genomic: GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG
EST: gi|18174948|gb|BM350336.1|BM350336
EST:     GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCA                         GAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG
genomic: GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGG

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), 47 (downstream exon)
Score: 223

GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 112

GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 62

GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 360

GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgccc ... ggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaatagcatgataataacattctctgtactaacagcacatgtggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT
                             tactaac  putative branch site (score: 360)
          atgataataacatt  TA-rich tract