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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttaagttcttcagaagcctttttcatgatcggttcaatttctgtttttcctaagacatgctattgttcgaattccactcagcacattactaacaatacgtttgaccttacgtaccaatatatcatcaccacatctctttttacattgtgaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG

Basic information

species Zea mays
transcript GRMZM2G169089_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169089_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 3'ss of exon 13
gtactttaagttcttcagaagcctttttcatgatcggttcaatttctgtttttcctaagacatgctattgttcgaattccactcagcacattactaacaatacgtttgaccttacgtaccaatatatcatcaccacatctctttttacattgtgaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG
                  ||    ||| ||     | ||  |   || |  || ||||       | |  ||  |   |  || |  |  ||| | | || | | |    | |        |||| | || |    || || || | | || |  |||  ||| ||||| |||| || || ||||||||||| |||||||||||||||  ||||||||||||||||
----------------gtaaattctttccaca--tgcttagag--ctatcatttctaa-------tttcttttcaccactccttatgattttattgaaaa-atgctctggcatgtaatttcatatgt-attatt-tatttcattgtcc-ttatcgatttgcagCTATGTGTTGCTGTTCCATGCCACATTTTTAAATTCTGGGCATTTATTGGGATCATGTTTCAG
















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|18164197|gb|BM334036.1|BM334036
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|17930011|gb|BM266971.1|BM266971
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18165097|gb|BM334936.1|BM334936
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|32929949|gb|CF034761.1|CF034761
EST:     GGTGTAGCTATTCTAATCTCGGTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18172967|gb|BM348355.1|BM348355
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|113703224|gb|EE680728.1|EE680728
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|261490382|gb|GO359873.1|GO359873
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18168645|gb|BM338485.1|BM338485
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18171503|gb|BM341343.1|BM341343
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18162243|gb|BM332082.1|BM332082
EST:     GTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTATGGGCATTTTCTGGG
genomic: GTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|17929613|gb|BM266573.1|BM266573
EST:     CTCGTTTCTGGTNTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: CTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|16921463|gb|BM075161.1|BM075161
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18166090|gb|BM335929.1|BM335929
EST:     CAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: CAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|17930787|gb|BM267747.1|BM267747
EST:     GGTGTAGCTAATCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTATGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18166675|gb|BM336514.1|BM336514
EST:     GGTGTAGCTAATCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG

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: 44 (upstream exon), 45 (downstream exon)
Score: 13

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 32

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 35

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttacgtaccaatatatcatcaccacatctctttttacattgtgaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG
 accttac  putative branch site (score: 35)
            aatatatcat  TA-rich tract