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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagacctgtattgtttcagatatcctctattttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcagtcagctgtacaat...

Basic information

species Zea mays
transcript GRMZM2G023289_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 16
AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatg----tagacctgtattgttt---------cagatatcctctattttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcagtcagctgtacaat---------------------------------------------------------
 || ||||| || || ||||||||||| |||||||| |||||||| ||||| |||||||| |||||  |||| |||||||||||||||||||| || ||||||||     |  |   ||||||||            |||||||  ||||| | |||||||||||| |||| |   | |    ||       || |  | || | |||  |                                                           
TGTGGTTGCCGCAGATGAGTTTGAGTATAAGGATCCTGTTGATGGTTCTGTCTCCAAGCATCAGGGTGTCCGGTACCTCTTCGGAGATGGTTCCCGGCTGgtatggtcccattctgttattgtttgttgaccttataatatccttcattttgtttcttgaaccaaagcaaatgaagtagcac-aatttggcattgcaaattcgggtgtttatcgcagagtgtgagtgcaacaaatactggtgaactgaccattagttcctcaaattctag

upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 16
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 16
AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagacctgtattgtttcagatatcctctattttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcagtcagctgtacaat
 || |     || || ||||| |||||||| |||||||| ||||||||||| || |||||||| || ||||||||| | ||||  ||||| |||||||| ||| || ||  ||| |    |    |     | |||  |   | ||    |||    |    ||  |  |     |||||| | |  |      |  |  
TGTTGCAAGCGCAGATGAGTTCGAGTACAAAGATCCAGTAGATGGCTCTGTTTCAAAGCACCAAGGGATCCGATACTTATTCGAGGATGGATCACGACTTgtaagtcgatatgtgtgaaatggattcataacaattcaacaacctgtg--aaattgtaaaagctaatccggg---cttgtttctc--ttgttcatgaag-

upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 16
lower sequence: PP1S4_12V6.1 (Physcomitrella patens), 5'ss of exon 17
AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagacctgtattgtttcagat------atcctctatt----ttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcagtcagctgtacaat
 ||    | |||||||||||||||||| ||||||||||||||    ||  | ||||  |||||||| ||||| ||||| |||   |||||||| || |||||  ||     | | |  ||||||||      ||    || |    | ||   | |||   | || |    ||||| || | |  || ||  |  || |||         
GGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGACCAGTCCATATCCAGCCACCAGGGTATCCGCTACCTGTTCAAGGATGGTTCTCGGCTGgtgcgtttctatttctattttcagattgaaaaatttgttagtcccgtcattcttggaagtgagacgagacatctgg-gttagatgctggtatcagag-cagt--------

upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 16
lower sequence: PP1S168_70V6.1 (Physcomitrella patens), 5'ss of exon 17
AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagacctgtattgtttcagatatcctctattttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcag------tcagctgtacaat----
 ||    | ||| |||||||||||||||||||| ||||||||    || |||||    || ||||| ||||| || || |||   |||||||| || |||||| ||       |  | || || ||  ||     |||||   |   | ||   |||    |||  ||  |||| | |  || || |      ||   |  ||||     
GGTTCAAGAAGCAGACGAGTTTGAGTACAAGGACCCAGTTGACCAGTCCGTGTCTTGTCATCAGGGTATCCGTTATCTTTTCAAGGATGGTTCTCGGCTGgtacgt-------ttcttttccacattaccatgtctttattcgtgttatcattgcaat---tctcatgctaaaagcataatcggctggtttattcgttttcacaaacatg

upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 16
lower sequence: EFJ09195 (Selaginella moellendorffii), 5'ss of exon 15
AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagacctgtat-tgtttcagatatcctctattttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcagtcagctgtacaat
  |    | ||| ||||||||||||||||| |||||||||||||| || ||  | |  ||||| || ||||| |  || |||   ||||| || ||||| ||  ||| |      | | || || | |   | |     | ||| |   |        ||                                         
TATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGAATCCGCTTTCTTTTCCAGGATGGCTCTCGACTTgtgagtaaaggaaactctcttccacagagattgttaaaaacgtcgtccgcttcgtttcag-----------------------------------------

upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 16
lower sequence: EFJ05270 (Selaginella moellendorffii), 5'ss of exon 15
AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagacctgtat-tgtttcagatatcctctattttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcagtcagctgtacaat
  |    | ||| ||||||||||||||||| |||||||||||||| || ||  | |  ||||| || ||||| |  || |||   ||||| || ||||| ||  ||| |      | | ||||  | |   | | |   | ||| |   |        ||                                         
TATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGAATCCGCTTTCTTTTCCAGGATGGCTCTCGACTTgtgagtaaaggaaactctctttcgcagagattgtttaaaacgtcgtccgcttcgtttcag-----------------------------------------

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|78108858|gb|DV527275.1|DV527275
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|71426274|gb|DR807324.1|DR807324
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|5296174|gb|AI782854.1|AI782854
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTCTCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|211541121|gb|FL006422.1|FL006422
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|32906153|gb|CF010966.1|CF010966
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTCTCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|5895776|gb|AW037022.1|AW037022
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTCTCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|78024768|gb|DV493155.1|DV493155
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|31357336|gb|CD441693.1|CD441693
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTCTCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|67020139|gb|CO448888.1|CO448888
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|32850278|gb|CD989959.1|CD989959
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTCTCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|32914018|gb|CF018830.1|CF018830
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTCTCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|211190026|gb|FL186116.1|FL186116
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|149060808|gb|EE157260.2|EE157260
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|5081034|gb|AI738296.1|AI738296
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|78109659|gb|DV528075.1|DV528075
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
EST: gi|44900765|gb|CK827310.1|CK827310
EST:     TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTG                         GTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC
genomic: TGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagac ... ggcgttctagGTGTTCCGTCTATCCGGAACCGGTTCTGTTGGTGCCACCATCCGTGTCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGCATCCGATACCTCTTCGGAGATGGTTCACGACTGgtatgtagacctgtattgtttcagatatcctctattttatgtcttgaaccaaaacaaagggtctggtgtgaaaaccttgttccgcagtcagctgtacaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG