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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgttacccctcgtcttgcatatacgttgttacacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttctcagctctttttcgttgcatttttatgcag

Basic information

species Zea mays
transcript GRMZM2G047219_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047219_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 5'ss of exon 3
GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgttacccctcgtcttgcatatacgttgtt---acacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttc-tcagctctttttcgttgcatttttatgcag
||||||||||||||||| | ||||||||| ||||||||||||   |   | | |||||||| ||   || ||   ||   |        | ||||  | |    ||| |   |  | ||   || | ||    ||  ||     |   | || |  ||||||      |  | | |   | ||  || ||| |      ||||||||  ||| || ||| ||
GTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTGgtaaaacat---ctttgtcttgcagatggattctttgaacttgtttcttttcagctatgctgttctttaaaccagt--attatcaatgacttgttggt--ctagctagcatagctcctttttttttcagttaattcattccttgttcatgattcgtttatgttttttcgt--catcttcatgtag

upper sequence: GRMZM2G047219_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ29885 (Selaginella moellendorffii), 5'ss of exon 2
GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgttacccctcgtcttgcatatacgttgttacacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttctcagctctttttcgttgcatttttatgcag
||||||||||||||||| |||||||||||||||||||||||       |     || ||  | |   ||| |     || |   ||        |  |||      | ||  |  |||  |  |||   ||                                                                                       
GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaac--acaaagttcctgtttttttcttgctctctttcctccaca------catccgtgacgtgttcttagagcactttttcttttccag---------------------------------------------------------------------------------------

upper sequence: GRMZM2G047219_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ06085 (Selaginella moellendorffii), 5'ss of exon 2
GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaa-------atgttacccctcgtcttgcatatacgttgttacacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttctcagctctttttcgttgcatttttatgcag
||||||||||||||||| || ||||||||||||||||||||       | ||| |   |  | |        | ||  | |||| |||  |  || | || || | || | | | ||    | | |                                                                                                   
GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTGgtaagaacacaaagttcctgtttttttcttgctctctttcctccaca-catccgtgacgtgttcttagagc-acttttttcttttccag---------------------------------------------------------------------------------------------------

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|148955762|gb|EC901460.2|EC901460
EST:     AAGAATCAAATTGATGGGG                         TTAAGAGCATCGGGGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: AAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|50331999|gb|CO527125.1|CO527125
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211142589|gb|FL359509.1|FL359509
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGAGGA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGGAGGA
EST: gi|211529297|gb|FL356731.1|FL356731
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGAGGA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGGAGGA
EST: gi|17931616|gb|BM268576.1|BM268576
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|149015400|gb|EE045246.2|EE045246
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|74243388|gb|DT651302.1|DT651302
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCNAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|148966374|gb|EE017368.2|EE017368
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGG
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGG
EST: gi|12045929|gb|BF728159.1|BF728159
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211072521|gb|FL326767.1|FL326767
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|148996959|gb|EE035773.2|EE035773
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|76293497|gb|DV033065.1|DV033065
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|78180658|gb|DV550986.1|DV550986
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCAC
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCAC
EST: gi|32848760|gb|CD988441.1|CD988441
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211394348|gb|FL351051.1|FL351051
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGGAGT
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGG-AGG
EST: gi|89251955|gb|DY623741.1|DY623741
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|148966373|gb|EE017367.2|EE017367
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|6742502|gb|AW313317.1|AW313317
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|71774203|gb|DR972081.1|DR972081
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211267296|gb|FL319984.1|FL319984
EST:     -TGGATTGGATTGGCCAAAAGAATCAA-TTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGAGGA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGGAGGA
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgttacccctcgtcttgcatatacgttgttacacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttctcagctctttttcgttgcatttttatgcag

- - - - - - - -  AAAGAA
- - - - - - - - - - - - - - -  ATGCTG