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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAATGCGGCATCGGGCGAGCTTTTCTGTAGGTAGAAAATGGCTGACGCTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctaccgccgatttgttccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcag

Basic information

species Zea mays
transcript GRMZM2G047055_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047055_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 5'ss of exon 1
AACAAATGCGGCATCGGGCGAGCTTTTCTGTAGGTAGAAAATGGCTGACGCTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagct------accgccgatttgttccc-tgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcag
                             |   | | || ||||||||||| |||||||||||||||||||||||||| || |||||||| ||||||||||||||||      | | | |  | ||| || |  ||  ||    |    |||    |  |  |||         || || |||
-----------------------------GCTAGCATAAGATGGCTGACGCCGAGGATATCCAGCCCCTCGTCTGCGATAATGGAACTGGTATGGTCAAGgtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtggtttgtgtcag

upper sequence: GRMZM2G047055_T02 (Zea mays), 5'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 3
AACAAATGCGGCATCGGGCGAGCTTTTCTGTAGGTAGAAAATGGCTGACGCTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctaccgccgatttgttccctgaactaaac-------actta-ttcttcagaatc-----ccctaacaacaccaacttctggcag-----------
                          || |||  ||  |||||||||||| ||||||  | |||||| | || |||||||| |||||||| ||||||||||| || |  | |   |     ||    | |||         ||||  ||| |  || ||       |||  | |   | ||||||               
-------------------------GTCGGTAT-TAAGAAATGGCTGACGGTGAGGAAGTACAGCCCTTGGTGTGCGACAATGGAACTGGAATGGTCAAGgtgaggtcactcttctaaaacccagagattaacttttccgaacttggttcattggattcaaggattctataatcttgagcttctgctgaaaaatattcta
















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|149009778|gb|EE041676.2|EE041676
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148943327|gb|EC888385.2|EC888385
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148937756|gb|EC881963.2|EC881963
EST:     CCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148941700|gb|EC886651.2|EC886651
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|31353585|gb|CD437942.1|CD437942
EST:     TCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCTCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: TCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|29946699|gb|CB816281.1|CB816281
EST:     CCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|67010753|gb|CO439502.1|CO439502
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148995731|gb|EE034959.2|EE034959
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|31558647|gb|CD527859.1|CD527859
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|7844554|gb|AW787776.1|AW787776
EST:     ATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: ATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148982853|gb|EE028703.2|EE028703
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148930560|gb|EE285193.2|EE285193
EST:     CAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148941518|gb|EC886449.2|EC886449
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|111190762|gb|EE288898.1|EE288898
EST:     TGGCCTGGTCACC                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCCTT
genomic: TGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|149085206|gb|EE174712.2|EE174712
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|149078654|gb|EE167442.2|EE167442
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|149059474|gb|EE156959.2|EE156959
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|149014382|gb|EE043976.2|EE043976
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|149051760|gb|EE155884.2|EE155884
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148945800|gb|EC891086.2|EC891086
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148930172|gb|EC872554.2|EC872554
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|211098081|gb|FL308904.1|FL308904
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCTCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148947214|gb|EC892565.2|EC892565
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|8103118|gb|AW927778.1|AW927778
EST:     CTGA-GA-ATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|211523834|gb|FL034055.1|FL034055
EST:     CTGAGGATATCCAACCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|21330968|gb|BQ486349.1|BQ486349
EST:     CTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGCT
genomic: CTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|148950007|gb|EC895535.2|EC895535
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|149061171|gb|EE157430.2|EE157430
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|14701052|gb|BI233470.1|BI233470
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCTCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAATGCGGCATCGGGCGAGCTTTTCTGTAGGTAGAAAATGGCTGACGCTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctaccgccgatttgttccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT