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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagaattatgcatgaactgcttttgatattaatctgaccacacgcaccataggtccataacatgaatgtttattcttacaactctgattttcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG

Basic information

species Zea mays
transcript GRMZM2G108416_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 16
cagaattatgcatgaactgcttt--tgatattaatctgaccacacgcaccataggtccataacatgaatgtttattcttacaactctgattttcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
   |  | | |||||| | || |  | | ||  |  ||   | | |  | |||      ||     ||| |  ||| | | ||    | ||||||| ||||||||||||| || ||||| ||||||||||||||||||
-ctaccttttcatgaattactataataagatggacatgttgagatgttctataacatt-tacttgaaatctgaattttgataatgggggttttcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
















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|60357806|gb|DN224779.1|DN224779
EST:     TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG                         GTATGGACAACCGGAACAATGGGTGAAATCACACCG
genomic: TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
EST: gi|148969666|gb|EE020531.2|EE020531
EST:     TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG                         GTATGGACAACCGGAACAATGGGTGAAATCACACCG
genomic: TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
EST: gi|6827209|gb|AW330852.1|AW330852
EST:     TGTTACATGAACGACGCATTAGTCTGTCGGAATTCCATGCTGCAGATGAG                         GTATGGACAACCGGAACAATGGGTGAAATTACACCG
genomic: TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
EST: gi|211381070|gb|FL456665.1|FL456665
EST:     TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG                         GTATGGACAACCGGAACAATGGGTGAAATCACACCG
genomic: TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
EST: gi|149084134|gb|EE173537.2|EE173537
EST:     TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG                         GTATGGACAACCGGAACAATGGGTGAAATCACACCG
genomic: TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
EST: gi|60352318|gb|DN219291.1|DN219291
EST:     TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG                         GTATGGACAACCGGAACAATGGGTGAAATCACACCG
genomic: TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
EST: gi|12058174|gb|BF733074.1|BF733074
EST:     TGTTACATGAACGACGCATTAGTCTGTCGGAATTCCATGCTGCAGATGAG                         GTATGGACAACCGGAACAATGGGTGAAATTACACCG
genomic: TGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG

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: 144

GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 179

GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtact ... tcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accataggtccataacatgaatgtttattcttacaactctgattttcacgtgcagGTATGGACAACCGGAACAATGGGTGAAATCACACCG
                                          ttttcac  CT-rich tract
                   aatgtttattctta  TA-rich tract