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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagttgatttacttcatgcagtgaggttcctgattatattgaaacaaatggttctgtgcggtttaatacatcctatttttctttttgaatagaaa...

Basic information

species Zea mays
transcript GRMZM2G023652_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023652_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g36340.1 (Oryza sativa), 5'ss of exon 8
AGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagttgatttacttcatgcagtgaggttcctgat-tatattgaaacaaatggttctgtgcggtttaatacatcct-atttttctttttgaatagaaa-
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AGAGGCTGAGATCAAATTACTTAGGAAGAGCCTGACATTTAAAGCGACACCCATGCCAAGCTTTTACAAGGAGCAACCTCCTAAAGTTGAGTTGAAAAAGgtactaagataa---acttgatcttgcaaagttgctgatatctgttggcaaaaaaaaatccacattattcaagacttctagagttctagactgcaatatcctc
















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|31355088|gb|CD439445.1|CD439445
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|32838814|gb|CD978495.1|CD978495
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAG
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAG
EST: gi|22819173|gb|BU499263.1|BU499263
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|60357341|gb|DN224314.1|DN224314
EST:     CAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|22819288|gb|BU499378.1|BU499378
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|21809702|gb|BQ668020.1|BQ668020
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|21843366|gb|BQ703947.1|BQ703947
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|32833164|gb|CD972842.1|CD972842
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAG
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAG
EST: gi|26559955|gb|CA832190.1|CA832190
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAA-                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|87157517|gb|DY402306.1|DY402306
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|21891697|gb|BQ744910.1|BQ744910
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|32839274|gb|CD978955.1|CD978955
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGC
EST: gi|7217064|gb|AW563186.1|AW563186
EST:     AAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGNTAGGTCGCCAAAGCTCGGCCGGCCCAAGCCAGCC
genomic: AAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|31355396|gb|CD439753.1|CD439753
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|60356563|gb|DN223536.1|DN223536
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|32837723|gb|CD977401.1|CD977401
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCG
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCG
EST: gi|22542624|gb|BU093062.1|BU093062
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|24769732|gb|CA404861.1|CA404861
EST:     CCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagttgatttacttcatgcagtgaggttcctgattatattgaaacaaatggttctgtgcggtttaatacatcctatttttctttttgaatagaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatagaa