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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgatgatgcagcctttcaccatgtgtaaaatataaatagcctccattaaatctgttattaaccactacatttctgacatgatgtcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT

Basic information

species Zea mays
transcript GRMZM2G100260_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100260_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 4
------gtaatatgatgatgcagcctttcaccatgtgtaaaatataaatagcctccattaaatctgttattaaccactacatttctgacatgatgtcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT
      ||||||| ||   |||    |   ||  |  |  || ||   ||  ||  | ||  | |||| |||   ||  | || || |  |||| |  | |||||||||||| || |||||||| || |||||||||||||| |||||||||||||| ||||||||| ||||||| ||||| || ||||||||||||||| ||||
gtaggagtaatataatacagcatttctagtcccagatttgaaaattcttaagctgtagtagctttgttgttattgacaccgttactaagctgatatactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT

upper sequence: GRMZM2G100260_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT4G18460.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------gtaatatgatgatgcagcctttcaccatgtgtaaaatataaatagcctccattaaatctgttattaaccactacatttctgacatgatgtcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT
                                || |||| |   |    || | | ||||    || ||   ||  |   ||   ||| ||  |  ||      |||    ||||     |  | |||| ||||| ||||| ||||||||  || |||| ||||| || ||||||||||| || || ||| ||||||  ||||||||||| || || || ||| ||||
gtaatgatgcatctctttattattcatataccatttgattagagaaaggtttagcttgtggtttatgtactgaggtttgttt---tct-ttgcttgccctggtctttggatcatgtgtgttaatacagTTAGTCAATTCACATTATACGGATTCTTGAAAGGTAACAAACCAGATTTTCATGTCGCAATGCCACCTGATAAAGCGAAACCTTTTTACGCCTCTTTAGT
















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|211144459|gb|FL048070.1|FL048070
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
EST: gi|211144465|gb|FL048076.1|FL048076
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
EST: gi|211144466|gb|FL048077.1|FL048077
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
EST: gi|211144461|gb|FL048072.1|FL048072
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
EST: gi|60344391|gb|DN211364.1|DN211364
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
EST: gi|211144462|gb|FL048073.1|FL048073
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
EST: gi|14701176|gb|BI233594.1|BI233594
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
EST: gi|211144469|gb|FL048080.1|FL048080
EST:     GTTATGCAGCGTAACTTTGAAGTGCTATTGG                         TCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC
genomic: GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTC

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: 31 (upstream exon), 45 (downstream exon)
Score: 84

GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT


Block sizes: 31 (upstream exon), 46 (downstream exon)
Score: 83

GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 73

GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 106

GTTATGCAGCGTAACTTTGAAGTGCTATTGGgtaatatgat ... tcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctccattaaatctgttattaaccactacatttctgacatgatgtcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT
                                           tgtcttcttc  CT-rich tract
      attaaatctgttatta  TA-rich tract