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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctagtctaacccacctacctaatagtaactgctgctacggaacaaaataactttctttgcttggattaggagatgggaaattgagacaatctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATGCAGACAACTCAGAAGGAGATAAGAAGACTAAGATTGGGTCTTTCAAGAA

Basic information

species Zea mays
transcript GRMZM2G174990_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174990_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 1
-----------atctagtctaacccacctacctaatagtaactgctgctacggaacaaaataactttctttgcttggattaggagatgggaaattgagacaatctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATGCAGACAACTCAGAAGGAGATAAGAAGACTAAGATTGGGTCTTTCAAGAA
           ||     |||| |  |  | | |    || | | |||   | || |||| || ||  |    |   |  | ||||||  |  |||          |||||| |||||||| |||   ||||| ||||||| |||||||| ||||||||| ||||||||||| |||||||| ||||||||||| ||||| |||||||||||
tattatttgtcattctccctaagcggctaagccacc--tatcagttgccg-gtaagaaaaaaagttcataccgtcataacatgagatgcta--ttg------ctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACGCAGACAACTCCGAAGGAGAGAAGAAGACTAAAATTGGTTCTTTCAAGAA
















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|101402477|gb|EB822801.1|EB822801
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|211480226|gb|FK977831.1|FK977831
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|60338296|gb|DN205269.1|DN205269
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|31997893|gb|CD661823.1|CD661823
EST:     GGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: GGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|1590775|gb|AA072437.1|AA072437
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|149084713|gb|EE174205.2|EE174205
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|161586771|gb|EY951293.1|EY951293
EST:     CGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: CGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|211483108|gb|FK977835.1|FK977835
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|71426247|gb|DR807297.1|DR807297
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|211480223|gb|FK977828.1|FK977828
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|28931255|gb|CB334616.1|CB334616
EST:     CCTCTCGA-CGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: CCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|211483115|gb|FK977842.1|FK977842
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|101386148|gb|EB815117.1|EB815117
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|31611997|gb|CD568619.1|CD568619
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
EST: gi|101402741|gb|EB822898.1|EB822898
EST:     TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCAT                         GCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG
genomic: TGTGCCGGCGGACGGGATGTCAGGCCCTCTCGACCGATTTGCTAGGCCATgtgagtatga ... atctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataactttctttgcttggattaggagatgggaaattgagacaatctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATGCAGACAACTCAGAAGGAGATAAGAAGACTAAGATTGGGTCTTTCAAGAA
 aaataac  putative branch site (score: 2)
                                              tctttgc  putative PPT
        tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctagtctaacccacctacctaatagtaactgctgctacggaacaaaataactttctttgcttggattaggagatgggaaattgagacaatctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATGCAGACAACTCAGAAGGAGATAAGAAGACTAAGATTGGGTCTTTCAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG