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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAATCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttcagttcatctatgctacctcctgaatgaaccaaactttgtataatttgatcacttcctcctgaatgaagcaaactttgtatagtttgatcac...

Basic information

species Oryza sativa
transcript LOC_Os05g41900.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G073535_T01 (Zea mays), 5'ss of exon 2
ACATAAAGACCAACGAGT-AAAAGCTTGATCTGTCCGGTGCCAACCAA---TCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacg------cttcagttcatctatgctacctcctgaatga-acca-aactttgtataatt--tgatcacttcctcctgaatgaagcaaact-ttgtatagtttgatcac-------------------------------------------------------------------------------
     |||| |||| | | |||||||||||| |  ||||||| || ||   ||||||| ||||||||||||||||||||||||| ||||||||||||||||| |||| |        ||| |||||  |||| |  |  |   | | |       |||  |||||   |     |||||  ||   |||||   | |  || |||| ||||| ||                                                                               
----TAAGAACAACAAATCAAAAGCTTGATCAGCTCGGTGCCTACAAAACCTCAACAACCAAGTTTCATGTCTGATCTCGACGTCCAGCTTCCATCTGCCTTTGgtatggctacttctcaattcatg-atgccatgtttttttttatattgtggttttacataatacatagcatcttccagcttcctgaagagtattactgaatagattgataacatcatacacacgaagttcatcttgaacatgcttattagtgttctgtttgcatctgatggtatggcatcatctttgatag

upper sequence: LOC_Os05g41900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G073535_T03 (Zea mays), 5'ss of exon 3
ACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAA---TCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacg------cttcagttcatctatgctacctcctgaatga-acca-aactttgtataatt--tgatcacttcctcctgaatgaagcaaact-ttgtatagtttgatcac-------------------------------------------------------------------------------
                        |||||| |  ||||||| || ||   ||||||| ||||||||||||||||||||||||| ||||||||||||||||| |||| |        ||| |||||  |||| |  |  |   | | |       |||  |||||   |     |||||  ||   |||||   | |  || |||| ||||| ||                                                                               
------------------------TTGATCAGCTCGGTGCCTACAAAACCTCAACAACCAAGTTTCATGTCTGATCTCGACGTCCAGCTTCCATCTGCCTTTGgtatggctacttctcaattcatg-atgccatgtttttttttatattgtggttttacataatacatagcatcttccagcttcctgaagagtattactgaatagattgataacatcatacacacgaagttcatcttgaacatgcttattagtgttctgtttgcatctgatggtatggcatcatctttgatag
















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|58588869|gb|CF987177.1|CF987177
EST:     AGAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|396941233|gb|HO188442.1|HO188442
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88326135|gb|CI651190.1|CI651190
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|33666834|gb|CF297801.1|CF297801
EST:     ATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGGGCGCTGGCCCTGGAGC
genomic: ATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCC--GGCGCTGGCCCTGGAGC
EST: gi|88976349|gb|CI024566.1|CI024566
EST:     ACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58587133|gb|CF985441.1|CF985441
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|29685126|gb|CB681401.1|CB681401
EST:     CGACGTTCAGCTTCCCTCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: CGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|86260752|gb|CI000200.1|CI000200
EST:     CTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: CTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|29687847|gb|CB684122.1|CB684122
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58591899|gb|CF990207.1|CF990207
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|29687846|gb|CB684121.1|CB684121
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58607649|gb|CK035682.1|CK035682
EST:     ACAAGCGAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|33692899|gb|CF321138.1|CF321138
EST:     GTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: GTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|89198573|gb|CI016658.1|CI016658
EST:     CTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: CTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAATCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttcagttcatctatgctacctcctgaatgaaccaaactttgtataatttgatcacttcctcctgaatgaagcaaactttgtatagtttgatcac

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