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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcgatggtgtagacaactttgtacatatatatgtatatttaattagctgtctgtttagttattgttattctgttatgtttatggccttacggg...

Basic information

species Oryza sativa
transcript LOC_Os07g47530.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47530.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G157621_T01 (Zea mays), 5'ss of exon 17
GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcgatggtgtagacaactttgtac-atatatatgtatatttaattagctgtctgt---ttagttattgttattctgttatgtttatggccttacggg
||||||  ||||||||| ||||||||||||||||| |  |||||  |||||||||| |||||||| |||||    |  || || || || |||||| ||  | ||| ||  | |||| |   || ||||    |||||   | |     |||   ||||   |    ||||  | ||   | |  |  ||    
GATGAAACGGAACTCTCCCAGTGGAAACAGCTATTGGGTCGTGACATTGAAATTCTTAAGGCAAAGGCTAATTTTTTGAAAATACAATCTgtaagtgtctgttgtgaagttagcttttttttatttatagacttatttgtgtggtgccttgtctgttagccttctgaattcaatgattggtgtaacacta----
















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|33797016|gb|CF324371.1|CF324371
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|58692536|gb|CK081223.1|CK081223
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|58690470|gb|CK079157.1|CK079157
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|29664460|gb|CB660735.1|CB660735
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|58690512|gb|CK079199.1|CK079199
EST:     GTGATGTTGAACTTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGAC
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGAC
EST: gi|33675839|gb|CF304078.1|CF304078
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|58658063|gb|CK046743.1|CK046743
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|33675419|gb|CF303658.1|CF303658
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|58660377|gb|CK049057.1|CK049057
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
EST: gi|33676430|gb|CF304669.1|CF304669
EST:     GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG                         TTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT
genomic: GTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcg ... ctggatgtagTTCTTAACCCGCAATGGTCTGGAATGTGCTGACATAGAGACATCAGCATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCGgtaagtatcgatggtgtagacaactttgtacatatatatgtatatttaattagctgtctgtttagttattgttattctgttatgtttatggccttacggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG