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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGCTTGACAGCGAGATTAAGTCTTGGCTTGCTTTTGCTGCCCAGAAGGTTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgtgtagttctcattttctgattcttaactagtcctttgcgtttcttttttcccttcatacattttcccttcatacaaacttattcattcttgcaaatttcatgtacag

Basic information

species Zea mays
transcript GRMZM2G149751_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149751_T06 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 7
TAAGCTTGACAGCGAGATTAAGTCTTGGCTTGCTTTTGCTGCCCAGAAGGTTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgtgtagttc-tcattttctgattcttaactagtcctttgcgttt---cttttttcccttcatacattttcccttcatacaaacttattcattcttgcaaatttcatgtacag----------
 ||||| || |||||||||||||| |||||||||||||||||||| || || ||||||||  |||| |||||||||||||||||||| || |||||||||||||||   | |  ||   | |||    ||||| | ||  |  || | |  |   | |  | | | | |  || |  |  || | | |||||| | |    ||  | ||||  || |||           
CAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTTTGCTGCCCAAAAAGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactcttttttgccctttatctattctcacctcttaattagagcctgagcatagtactcattactcaatagcatttga-agaaacttctgctcatttatacattt-gtgaacaatattgtacag

upper sequence: GRMZM2G149751_T06 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 6
TAAGCTTGACAGCGAGATTAAGTCTTGGCTTGCTTTTGCTGCCCAGAAGGTTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgtgtagttc---------tcattttctgattcttaactagtcctttgcgtttcttttttcccttcataca-------ttttcccttcatacaaacttattc----attcttgcaaatttcat-gtacag
 ||||| || |||||||||||||| ||||| |||||||||||||| ||||| ||||||||  |||| |||||||||||||||||||| || |||||||||||||||   | |  |||         | ||| ||| |    | | ||     |   | ||  || |     | || |        || | |       ||  |||| |     |   ||| |||    || ||||||
CAAGCTCGATAGCGAGATTAAGTCATGGCTCGCTTTTGCTGCCCAAAAGGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactctctttcaccctttatttattctctcacctcttagtaagagatcaggcttagttctcaatattattcggagaaacttctgctgctgctcaggcttacttttgtacatttgtaaacaatattgtacag
















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|32836434|gb|CD976112.1|CD976112
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|211445887|gb|FL403734.1|FL403734
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|32847674|gb|CD987355.1|CD987355
EST:     TGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTGCTTCGCAGCAAATGCTACTGCTCAGGCCTCGAGGAAATCCTCAGCC
genomic: TGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|211059641|gb|FL374513.1|FL374513
EST:     TTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGGGTCAAA-G-ATGAG                         GCTTACTTCGCANGCAA-TGCTGCTGCTCAGGCCTCGAGGAAATCCTCACC
genomic: TT-GAGGTTGATGCTCTTGCTAAGGCATTGGCTGG--TCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCA-GCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACC
EST: gi|211106464|gb|FL269547.1|FL269547
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAAGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAAGCCTCGAGGATATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|60358604|gb|DN225577.1|DN225577
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGC
EST: gi|211107371|gb|FL269554.1|FL269554
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCANGCCTCGAGGAAATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|211107368|gb|FL269551.1|FL269551
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|23199684|gb|BU582249.1|BU582249
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACC
EST: gi|211106466|gb|FL269549.1|FL269549
EST:     GTTGAGGTTGATGCTCTTGCTTAAG-CATTGGCCTG-TCAAAAAGATGAT                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
genomic: GTTGAGGTTGATGCTCTTGCT-AAGGCATTGGC-TGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|32833047|gb|CD972725.1|CD972725
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|18384329|gb|BM417528.1|BM417528
EST:     TTGTTGAGGTTGATGCTCTCGCTAAGGCATTGGCTGGTCAAA-GGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCG
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCG
EST: gi|211107370|gb|FL269553.1|FL269553
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
EST: gi|32845718|gb|CD985399.1|CD985399
EST:     TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAG                         GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC
genomic: TTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgt ... tcatgtacagGCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGCTTGACAGCGAGATTAAGTCTTGGCTTGCTTTTGCTGCCCAGAAGGTTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgtgtagttctcattttctgattcttaactagtcctttgcgtttcttttttcccttcatacattttcccttcatacaaacttattcattcttgcaaatttcatgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG