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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggtttttatatgacagcatcatataaacattatattttctgtattatgcttttttctgtctgtgtctgctgttcgtcacaactttatgacagtaaaaggcagacctatatatgtagtcactcatgcaaatgaaatctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAG

Basic information

species Zea mays
transcript GRMZM2G327394_T01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G327394_T01 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os08g22864.2 (Oryza sativa), 3'ss of exon 22
gtgaggtttttatatgacagcatcatataaa--cattatattt--tctgtattatgct---tttttctgtctgtgtctgctgttcgtcacaactttatgacagtaaaaggcagacctatatatgtagtcactcatgcaaatgaaatctc-----------tgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAG
||    ||||| | || ||| || |||||||   | |||   |  |||||||| || |    |  | | |   |  |||| ||| |  ||   ||| | |  |  ||  | || ||||  |   |  || |   ||||||| ||||  |           |||||||||| ||||||||||| ||||| || |||||||| ||||||||| || | ||||| ||||| || ||||| ||  | || ||||||||||| |||
gtagaatttttttctg-cagtatgatataaaacaaatatgcctcatctgtattttggtatagtcctttatactttactgcagtttgaaacggtttt-taatggataataggaggcctaattcattgctcgcatttgcaaataaaataccactactcttaatgcagGCTCTGGCAGCCATACCCTCAATTGACAGTGAAGCCGTCCAACAGAGAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG
















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|12968280|gb|BG265226.1|BG265226
EST:     TAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG                         GCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG
genomic: TAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG
EST: gi|113700911|gb|EE678415.1|EE678415
EST:     ACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG                         GCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGCCCAACAGCGATTG
genomic: ACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG
EST: gi|15499587|gb|BI596100.1|BI596100
EST:     ACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG                         GCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG
genomic: ACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG
EST: gi|211404353|gb|FL448257.1|FL448257
EST:     ACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG                         GCTCTTGCAGCCATACCTTCAATATATAGTGAAGCAGTCCAACAGCGATTG
genomic: ACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG
EST: gi|15499586|gb|BI596099.1|BI596099
EST:     TATGCAGGAATTCGATAGCTCTGGAACAG                         GCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG
genomic: TATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTG

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), 45 (downstream exon)
Score: 118

GCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 104

GCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 70

GCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 125

GCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAGgtgaggtttt ... atctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtaaaaggcagacctatatatgtagtcactcatgcaaatgaaatctctgcagGCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAG
                                              tctctgc  CT-rich tract
                 tatatatgta  TA-rich tract