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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatacctcaactcaactgtacagtttattaacccttctaataagcagctgccagtctttctgacgtaatagtaaagaaaaaaatgttctttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG

Basic information

species Zea mays
transcript GRMZM2G065012_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 12
-----------------------------------------------------------------------------ttgatacctcaactcaactgtacagtt--tattaacccttctaat--aagcagctgccagtctttctgacg--taatagtaaagaaaaa----------aatgttctttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG
                                                                              ||     | |    ||   |  | ||  | || ||  ||| | |  |  ||      |||   | ||  |  | | || ||| ||  |           |     || |  |||||| |||||||| || ||||||||||| |||||||| |||||||| |||||||||||||||||||||||||| ||||||||
gtgagtgttattgctatccctttatagtgtgataacatattccattttcatcctctttatgcataggaaaaaaaatcatggagtgtgataagaaacattgatttgttttttacatttcaagtggagacaaaaaagagtagctatgttgattgaaagcaaataacgactttgcttctgacaaatttatcctcagCTCATGAGAGTCTATGGAGCACTGCTATGGTCGCTTGGGAAAGTTCTGAACACACCAGAAGTCATGCGTGTGTACATAGG

upper sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT4G05520.1 (Arabidopsis thaliana), 3'ss of exon 12
ttgatacctcaactcaactgtacagtttattaacccttctaataagcagctgccagtctttctgacgtaatagtaaagaaaaaaatgttctttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG
  |  |  |    |     || |  || |||     |  | ||||||         || || | ||  | |  | |              |||| |  |||| ||||||||||| |||||| || |||||||||| || |||||||||||||||||||| ||| | |||||||| || ||
--gtaagtttcgttt--tcgtcccattcatttgttatgttcataagct--------tcatttttactcattgttgagccg--------ctttttctaaagCTAATGAGAGTGTATGGAGCATTGATGTGGTCGCTTGGTAAAGTCCTGAACACACCAGAGGTCGTACGTGTCTATATTGG
















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|149102174|gb|EE287594.2|EE287594
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAG                         CTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
EST: gi|50323441|gb|CO518567.1|CO518567
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAG                         CTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
EST: gi|211180215|gb|FK950406.1|FK950406
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAG                         CTGATGAGAGTGTACGGAGC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGC
EST: gi|22545340|gb|BU097699.1|BU097699
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAG                         CTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
EST: gi|116827521|gb|EC871429.1|EC871429
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAG                         CTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
EST: gi|78124010|gb|DV542394.1|DV542394
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAT                         CTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGAGAAAGTCCTGAAC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
EST: gi|211180217|gb|FK950408.1|FK950408
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAG                         CTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
EST: gi|211180216|gb|FK950407.1|FK950407
EST:     ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAG                         CTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC
genomic: ACAAGATACGCATAGTTCTCAACAAGGCCGACCAAGTTGATGCACAGCAGgcgagtattg ... tttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagctgccagtctttctgacgtaatagtaaagaaaaaaatgttctttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG
              ttctgac  putative branch site (score: 2)
                                        tgttctttttttc  putative PPT
                      taatagtaaagaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatacctcaactcaactgtacagtttattaacccttctaataagcagctgccagtctttctgacgtaatagtaaagaaaaaaatgttctttttttcagCTGATGAGAGTGTACGGAGCACTGCTGTGGTCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT