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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCTCCAGAGCTGTGCTGGTTCTCCAGCAGAACCTAACTCCGTTTGCGAAGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttttgcacaccaagaagaagctactactccaatttgaccggcagcaccgttgcttggtccgcgcgcgcatatgctgttgtgcaatgatctcttgtgttttgttatttctgataactgaagcaatcgacag

Basic information

species Zea mays
transcript GRMZM2G476009_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G476009_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g59140.1 (Oryza sativa), 5'ss of exon 2
CGTCTCCAGAGCTGTGCTGGTTCTCCAGCAGAACCTAACTCCGTTTGCGAAGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttttgcacaccaagaagaagctactactccaatttgac-cggcagcaccgttgcttggtccgcg-cgcgcatatgctgttgtgcaatgatctct-tgtgttttgttatttctgataactgaagcaatcgacag
|||||||||||| ||  ||||||| || |||||||| ||||| ||||| | ||| |||||   |||  | ||||| ||||||||  |||||||||||||||| |||  |      | ||| ||||||||| | |  | |||     |  ||   |  ||  ||  ||| |   | |||  ||   ||   |    ||  ||   || | || |   | |  |  |||      |  |   
CGTCTCCAGAGCGGTATTGGTTCTTCAACAGAACCTCACTCCATTTGCAAGGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg-----aacaacaagaagctattgcctctattcagttcaacaatcctattcttttttccccaatgagcac-tggcatttcacctaaatggctacatgatatgctgcctatatt--ctgtttttttttag--
















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|149013010|gb|EE042745.2|EE042745
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|5499455|gb|AI855322.1|AI855322
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|32849119|gb|CD988800.1|CD988800
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|32941255|gb|CF046074.1|CF046074
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|10191490|gb|BE761566.1|BE761566
EST:     CATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: CATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|78124667|gb|DV543051.1|DV543051
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|16925901|gb|BM078969.1|BM078969
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|37388912|gb|CF631671.1|CF631671
EST:     AGTCGTTTCTCATAGAGTTGGAGCCAAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|14243487|gb|BG841206.2|BG841206
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|120480234|gb|EH210778.1|EH210778
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|71762794|gb|DR960731.1|DR960731
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTTCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|149001167|gb|EE038432.2|EE038432
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|5871454|gb|AW017925.1|AW017925
EST:     AGTCGTTTCTCATAGAGTTGGAGCCAAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|211038261|gb|FL216363.1|FL216363
EST:     AGTCGTTTCTCATAGAGTTGGAGCCAAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|13490733|gb|BG517497.1|BG517497
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTT
EST: gi|149001168|gb|EE038433.2|EE038433
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCAT
EST: gi|13316032|gb|BG410479.1|BG410479
EST:     AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAG                         GAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTG
genomic: AGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttt ... caatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCTCCAGAGCTGTGCTGGTTCTCCAGCAGAACCTAACTCCGTTTGCGAAGTCGTTTCTCATAGAGCTGGAGCCGAAGATCCATCTGGAAATTTTCCAGgtcagttttttgcacaccaagaagaagctactactccaatttgaccggcagcaccgttgcttggtccgcgcgcgcatatgctgttgtgcaatgatctcttgtgttttgttatttctgataactgaagcaatcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA