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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtttgtgccttacaatgttttgttctattcttctgtggccttatccatgggcggtattttcactttgttttgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC

Basic information

species Zea mays
transcript GRMZM2G072156_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G072156_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g58590.1 (Oryza sativa), 3'ss of exon 12
gtaagcgtttgtgccttacaatgttttgttctattcttctgtggccttatccatgggcggtattttcactttgttttgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC
|||||| | | | ||     || ||    | || || | |   |  | ||            |  | ||| |||||| |||  ||||||||||||||||| ||||||||||||||||||||||| |||||||| |||||||| || || || |||||||||||||| |||||||||||||||||||
gtaagcctctattcccat--atcttcaaatttaatcctgtagagtttcatgggcacttcacttaattactctgttttcttcaccagGCTTTCCGTATTGTCAACAAGGAGTGGGAATACTCACATAAGAAGGGCTTCAAGTGCACATTCGAACGTGGGATTCTCCACCTCTATTTCAACTTCAAGC

upper sequence: GRMZM2G072156_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 9
gtaagcg-tttgtgccttacaatgttttgttctattcttctgtggccttatccatgggcggtattttcactttgttttgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC
|| || | ||||| |||     | || |  | | || ||  ||  || | |   |  |    ||  |   | ||| |   |   |||||||| || ||||| |||||||| ||||| || ||||||||||| || ||||||||||| || ||||| || || || ||| | ||||||||||| ||| 
gtgagtgatttgttcctcgttgttttcttgtttgttttttggtttccgtgttgctaag----atggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA

upper sequence: GRMZM2G072156_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ21082 (Selaginella moellendorffii), 3'ss of exon 9
gtaagcg-tttgtgccttacaatgttttgttctattcttctgtggccttatccatgggcggtattttcactttgttttgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC
|| || | ||||| |||     | || |  | | || ||  ||  || | |   |  |   |  | |   | |||||       |||||||| || ||||| |||||||| ||||| || ||||||||||| || ||||||||||| || ||||| || || || ||| | ||||||||||| ||| 
gtgagtgatttgttcctcgttgttttcttgtttgttttttggtttccgtgttgctaag--atggtgtgtgtgtgttt------gcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA

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|60353221|gb|DN220194.1|DN220194
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
EST: gi|87151911|gb|DY396700.1|DY396700
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
EST: gi|88752979|gb|DY537120.1|DY537120
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAGGGGGTTC
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
EST: gi|22491378|gb|BU051301.1|BU051301
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
EST: gi|19351533|gb|BM896065.1|BM896065
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
EST: gi|161591278|gb|EY959489.1|EY959489
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGG
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGG
EST: gi|148951030|gb|EC896684.2|EC896684
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTC
EST: gi|19351870|gb|BM896402.1|BM896402
EST:     GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATT                         GCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGG
genomic: GAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGG

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: 146

GGACAAATCGAAAGCACCAACATACAGTATAGAGAAAGATGGAAGCGCCGGAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GGACAAATCGAAAGCACCAACATACAGTATAGAGAAAGATGGAAGCGCCGGAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

GGACAAATCGAAAGCACCAACATACAGTATAGAGAAAGATGGAAGCGCCGGAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

GGACAAATCGAAAGCACCAACATACAGTATAGAGAAAGATGGAAGCGCCGGAGAGACTTGCTTCATAAGATTTCACGCTGGACCTCCATACGAGGATATTgtaagcgttt ... tgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttctgtggccttatccatgggcggtattttcactttgttttgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC
                               ttttcactttgtttt  CT-rich tract
                             tattttca  TA-rich tract