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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattcctattctggcccagtcttgaaattgcaagtggtccctctgattttgacctaattattataaatttgagctgaagtgattatactactacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAATTTGAAGAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGG

Basic information

species Zea mays
transcript GRMZM2G172101_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 3
-cattcctattctgg-cccagtcttgaaattgc-aagtggtccctctgattttgacctaattattataaatttgagctgaagtgattatactactacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAATTTGAAGAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGG
 |||  | ||| |||  ||| |  |  || ||  ||   ||| |||||| ||      ||  |||||  |  | || || || ||||       |  ||| |||||||||||  ||||||||||||||  |||||||||||  | || |  |||||||||||||||||||| ||||||| ||||||||||||||| || ||||
tcatggcaattatggatccaattgtacaaatgtgaaacagtcgctctgaattcctttgaa--attatctacgt-agatgtagagattgattccttctttgcagGCAAACAATTTAATTGTACGGACATGGGGAGAGAAGAGGATGGAAGGGAATTTGAAGAATCACGTGGATCTTTGCAAGATGCTTGACATTGTAGCTTTGG

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 3
---cattcctattctggcccagtcttgaaattgcaagtggtccctctgattttgacctaattattataaatttgagctgaagtgattatactactacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAATTTGAAGAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGG
      |  |  | || || | | | ||||||  ||   |   | |||| ||   |  ||  |||||| || | || |  || ||||       |  |||||||| ||||||  ||||||||||||||  ||||||| |||  | ||||  |||||||||||||||||||| ||||| | |||||||||||| || || ||||
ttgtggtttttctatgtccaattgtagaaattcgaaacagatgccctgaattcctctgaa--attatatatct-agatatagagattgattctttctttgtagGCTAACAATTTAATTGTACGGACATGGGGAGAGAGGAGGCTGGAGGGTAATTTGAAGAATCACGTGGATCTTTGTAAGATGCTTGACATAGTAGCTTTGG
















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|211021857|gb|FL368551.1|FL368551
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
EST: gi|18171951|gb|BM347339.1|BM347339
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATT-GGAGAGAAGAGAGTAGAGG
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGG
EST: gi|148937654|gb|EC881846.2|EC881846
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
EST: gi|31351150|gb|CD435507.1|CD435507
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCTCCGACGACGAG                         GCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
EST: gi|37421408|gb|CF648402.1|CF648402
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
EST: gi|18174283|gb|BM349671.1|BM349671
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATT-GGAGAGAAGAGAG
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAG
EST: gi|148931370|gb|EC874280.2|EC874280
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAAT
EST: gi|28985482|gb|CB350662.1|CB350662
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATT-GGAGAGAAGAGAGTAGAGG
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGG
EST: gi|18164364|gb|BM334203.1|BM334203
EST:     CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAG                         GCAAACAATAAAATTGTACGGACATT-GGAGAGAAGAGAGT
genomic: CGACGATTGGGAACATCGTGCATGAGTCCGTGCCAGTCAGCGAAGACGAGgtgatctgga ... ctacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgacctaattattataaatttgagctgaagtgattatactactacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAATTTGAAGAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGG
      acctaat  putative branch site (score: 3)
      acctaattattataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattcctattctggcccagtcttgaaattgcaagtggtccctctgattttgacctaattattataaatttgagctgaagtgattatactactacttgtagGCAAACAATAAAATTGTACGGACATTTGGAGAGAAGAGAGTAGAGGAAAATTTGAAGAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG