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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgattggagctactctatttgcacaatggtcataacatttctactgaacttatgctgcattaatgtttctctag

Basic information

species Zea mays
transcript GRMZM2G153569_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153569_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 5'ss of exon 2
TTTCTTGAGGGC-AGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgattggag--------ctactctatttgcacaatggtcataacatttctactgaacttatgc--tgcattaatgtttctctag
 ||||||||||  ||||||| ||||||||  | || || | | | |||||||| || |||||||| |||||||||||||||||||||||||||||| |||||||| ||||  | |        | ||  ||||| |  ||| | |||   || |  |||| |||||  |  | || | || | | || ||
-TTCTTGAGGGGGAGATGGCGGTTTCTTTCACCAACGTTAGCTCAGAGGCAGGCCTCAAAAAGCTCGATGAGTACCTTCTCACTCGCAGCTACATCTCTGGgtatatgatcagtgtccactgtccaccttattttctgaattgccatt-tatgttcactggacttaaacccttcaattatctgtttccag

upper sequence: GRMZM2G153569_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G17930.3 (Glycine max), 5'ss of exon 1
TTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgattggagcta--ctctatttgcacaatggtcata-acatttctactgaacttatgctgcattaatgtttctctag------------------
              ||||| ||  |  |     |  | | | |     | ||| |||| || |||||||||||||||||| | ||||| |||||||| |||||||| | ||    ||  ||   |||| |   |  |  |  | |  ||  |    |||| |    |   | | ||   | |                  
--------------ATGGCAGTCACACTCTACGACCTTAGCTCTTCCTCTGGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcactgcttttatgcttcgtttgtatgttttttttttataaatcctcgtttcttaagtgataaacaagctttaatggctattacagtattaggaa

upper sequence: GRMZM2G153569_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G37120.2 (Glycine max), 5'ss of exon 2
TTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgattggagctactctatttgcacaatggtcataacatttctactgaacttatgctg-cattaatgtttctctag----------------------
  | |  ||     ||||| ||  |  |     |  | | | | |   | ||| |||| ||||||||||||||||||||| | |||||||||||||| |||||||| | ||    || |    ||     |   |  ||| || |        | | |     ||||  |   | | ||                       
CGTATATAGCAAGCATGGCAGTCACACTCTACGACCTTAGCTCTGCCTCTGGGTTGAAGAAGCTTGATGAGTACCTTCTCCCACGCAGCTACATCACCGGgtatgtcactgcttttatt--gcttatgtgaatattttaaaatattagacaggcgtgtaaaatcattgcttgctttttacatattgtttgaaaagagaaatc

upper sequence: GRMZM2G153569_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G17930.4 (Glycine max), 5'ss of exon 2
TTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgattggagcta--ctctatttgcacaatggtcata-acatttctactgaacttatgctgcattaatgtttctctag------------------
| | |  ||     ||||| ||  |  |     |  | | | |     | ||| |||| || |||||||||||||||||| | ||||| |||||||| |||||||| | ||    ||  ||   |||| |   |  |  |  | |  ||  |    |||| |    |   | | ||   | |                  
TATATATAGCAAGCATGGCAGTCACACTCTACGACCTTAGCTCTTCCTCTGGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcactgcttttatgcttcgtttgtatgttttttttttataaatcctcgtttcttaagtgataaacaagctttaatggctattacagtattaggaa

upper sequence: GRMZM2G153569_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT2G18110.1 (Arabidopsis thaliana), 5'ss of exon 2
---TTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgt----atgtgatt----ggagctactctatttgcacaa-tggtcataacatttctactgaacttatgctgcattaatgtttctctag----------------
      ||| ||     ||||| |   ||||  | ||  ||||| | |   | ||  |||| ||||| |||||| | |||||||||||||| |||||||||||||    || || ||     | |||     | ||    |  | ||  | | |        | |   ||       |  ||| ||||||                 
TTCGAGCTTTAGAAACAATGGCGG---CTTTCCCCAACCTCAACTCTGGCTCCGGATTGAAGAAGCTCGATGAGCATCTTCTCACTCGCAGTTACATCACTGGgttagaatctgttttctaagggctgtctcaattatctatcttgttttgaaacaatagtagtaaccattactttcttctgtctctctatgtatgtatgtttatag

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|211378085|gb|FL329648.1|FL329648
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|76285318|gb|DV024886.1|DV024886
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|13237021|gb|BG355035.1|BG355035
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|61117414|gb|DN558375.1|DN558375
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGTTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|211291795|gb|FL131038.1|FL131038
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|76926349|gb|DV170823.1|DV170823
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|67012865|gb|CO441614.1|CO441614
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|33093219|gb|CF053213.1|CF053213
EST:     TTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGTTGA
genomic: TTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|32846492|gb|CD986173.1|CD986173
EST:     TACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGTTGA
genomic: TACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|31557965|gb|CD527177.1|CD527177
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|211291796|gb|FL131039.1|FL131039
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|211437727|gb|FL330573.1|FL330573
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|67037468|gb|CO464282.1|CO464282
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|32829957|gb|CD969635.1|CD969635
EST:     ACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGTTGA
genomic: ACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|211535307|gb|FL356762.1|FL356762
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|67016304|gb|CO445053.1|CO445053
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|8273074|gb|BE012169.1|BE012169
EST:     TCACTC-CAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: TCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|84977404|gb|DW475826.1|DW475826
EST:     GGGCTGAAAAAGCTTGATGGGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGTTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|211255757|gb|FL351785.1|FL351785
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|211232671|gb|FL320353.1|FL320353
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|60359229|gb|DN226202.1|DN226202
EST:     GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGG                         CTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
genomic: GGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA
EST: gi|33093139|gb|CF053133.1|CF053133
EST:     GTACCTCCTCACTCGCAGCTACATCACTGG                         CTACCAAGCATCCAAGGATGACCTGGCCGTCTACTCTTCATTTTTGGTTGA
genomic: GTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgatt ... gtttctctagCTACCAAGCTTCCAAGGATGACCTGGCTGTCTACTCTTCATTTTTGGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGCAGCTACATCACTGGgtatgtgattggagctactctatttgcacaatggtcataacatttctactgaacttatgctgcattaatgtttctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT