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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattccttcgtccacgtctcctcgtcatcctcatcctctctgccgctatagcttattatgccgcttcctggacggacctgaacgatggcctgctttgcttctctgccgcagcag

Basic information

species Zea mays
transcript GRMZM2G146463_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146463_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g26900.1 (Oryza sativa), 5'ss of exon 9
CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattccttcgtccacgtctcctcgtcatcctcatcctctctgccgctatagcttattatgccgcttcctggacggacctgaacgatggcctgctttgcttctctgccgcagcag
|||||||  ||||||||||   |||||||||| |||| | |||||||||||||||||||||||||||  |              |  |||| ||| | || || |||  |  | | |    ||| ||    ||  |||   |   || |    |  |||||                     
CATGCTGAGCAACATCGACAGCAACGACGCCTCCGCCAGCTACGCCAAGCCCGGCGGCTGGAACGgtatagc------------tggcctcctcaccttcgtcgtcttcgttgatctgctatat-atctgtctgtctgtctgtctctaatttgttccctgcag-------------------
















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|78113279|gb|DV531671.1|DV531671
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCNAGCCCGGCGGCTGGGACG                         ACCCTGACATGCTGGAGGTCGGGGACGGAGGCATGGCGTACAACGAGTACG
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
EST: gi|23199550|gb|BU582115.1|BU582115
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG                         ACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
EST: gi|22472587|gb|BU037067.1|BU037067
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG                         ACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
EST: gi|26560002|gb|CA832237.1|CA832237
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG                         ACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
EST: gi|22935898|gb|BU572173.1|BU572173
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG                         ACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG                         ACCCTGACATGCTGGAGGT
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGT
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     GACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCCGGCGGCTGGAACG                         ACCCTGACATGCTGG
genomic: GACCTGAACGACGCCTACGCCCGGTACGCCAAGCCC-GGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGG
EST: gi|26559550|gb|CA831785.1|CA831785
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG                         ACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGTACG
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCNAGCCCGGCGGCTGGAACG                         ACCCTGACATGC
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGC
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG                         ACCCTGACATGC
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGC
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     GACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCCGGCGGCTGGAACG                         ACCCTGACATGCTG
genomic: GACCTGAACGACGCCTACGCCCGGTACGCCAAGCCC-GGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTG
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     CGACCTGAACGACGCCTACGCCCCGTACGCCCAGCCCGGCGGCTGGAACG                         ACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGT
genomic: CGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattcct ... gccgcagcagACCCTGACATGCTGGAGGTCGGGAACGGAGGCATGGCGTACAACGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACGgtcaattccttcgtccacgtctcctcgtcatcctcatcctctctgccgctatagcttattatgccgcttcctggacggacctgaacgatggcctgctttgcttctctgccgcagcag

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