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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcctgcactgcttgcttgcttgcttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG

Basic information

species Zea mays
transcript GRMZM2G126900_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126900_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 4
--gtatggcctgcactgcttgcttgcttg----------cttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG
     |     | | | || |  |    |             | || | || ||   |    | |        | |||  |       | || |||||||| |||||||||||||||||||| || ||||| ||||||||||| |||||| | |||||||
caacctctttggaattactcggctaaaggaagaaagaaatgaaatggcaatacagtggggcacacttgtgacgtgtaacatgttctcttttctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG

upper sequence: GRMZM2G126900_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G14520.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatggcctgcactgcttgctt--gcttgcttac-tgccgatg-caactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG----------------------------------------
   |    |  ||| | || ||  | ||| | || |    ||  |   |  ||     | | || | |  |     |   ||| | |  |||| || || || || || || ||| |    || || |||||||||||||||||||||||||                                        
--gtaaattatactccctgattcggtttgatcacgttaaaatatcgtttaccggtttaatgattttgtgtttggtgtgtatgtgaat--cagATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGGCTGTCGTCGGTGATACATTTCCAGTGGGATGTGCTTTTGATGAATCTAT
















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|31363556|gb|CD447913.1|CD447913
EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
EST: gi|78119916|gb|DV538300.1|DV538300
EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
EST: gi|60396286|gb|DN229155.1|DN229155
EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
EST: gi|154130490|gb|EC872226.2|EC872226
EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
EST: gi|15554177|gb|BI644175.1|BI644175
EST:     CCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGNGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
EST: gi|76923453|gb|DV169495.1|DV169495
EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG
                                    aactcac  putative branch site (score: 2)
                                             tcattttc  putative PPT
                              taatctaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcctgcactgcttgcttgcttgcttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT