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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCACATCGGCATCGTGCTGGCCGCGCTGTGGGCCGCGGGCTCCCTCGGCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgctcttctgccgctgccgcccgcgcctctcgctgataagttgatgcgacttttttttttatcttttttgagctcctttacggcatatgcttag...

Basic information

species Oryza sativa
transcript LOC_Os01g14050.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14050.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G144403_T01 (Zea mays), 5'ss of exon 2
GTACCACATCGGCATCGTGCTGGCCGCGCTGTGGGCCGCGGGCTCCCTCGGCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgctcttctgccgctgccgcccgcgcctctcgctgataa--gttgatgcgacttttttttttatcttttttgagctcctttacggcatatgcttag
 |||||||||||  | |||||||||||||| |||||||| | | || |||||||||||  |||| |||||| ||||||||||||||||||||||||||||||  ||| |||  ||||| || || |   | |||| ||     |    || |  |  |    ||      |  ||||  |  |       | | |   |  |
CTACCACATCGGTCTGGTGCTGGCCGCGCTCTGGGCCGCCGCCGCCGTCGGCTTCCGCGGCTCCCTCCTCTACCTCCTCGCCTTCCTCTACCTCTACATGgtg-ggtactcg-ctgccacttcctctgccccctcacgtacgcactcattaaaacaccaggattcggcccccctttttcggccagaggaagaacacagtacg
















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|88368176|gb|CI575058.1|CI575058
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88431214|gb|CI574385.1|CI574385
EST:     GCTTCCGCCATTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACCATGAAGA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAAC-ATGAAGA
EST: gi|58690106|gb|CK078793.1|CK078793
EST:     CTTCCTCCT--CCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: CTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88694531|gb|CI738569.1|CI738569
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88734354|gb|CI757862.1|CI757862
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88763700|gb|CI773119.1|CI773119
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88389854|gb|CI626623.1|CI626623
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88449626|gb|CI579906.1|CI579906
EST:     CTTCCGCCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTAAATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAAAATGAAGAA
genomic: CTTCCGCC-ACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88743560|gb|CI767068.1|CI767068
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88410896|gb|CI578702.1|CI578702
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGGGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|117233805|gb|CT847747.1|CT847747
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88358378|gb|CI606887.1|CI606887
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88397069|gb|CI593281.1|CI593281
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTAAATG                         GTAAATGCTCGCTGTGCAATGAAATTGGGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88368269|gb|CI575151.1|CI575151
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
EST: gi|88445398|gb|CI584511.1|CI584511
EST:     GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATG                         GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA
genomic: GCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 43 (upstream exon), 73 (downstream exon)
Score: 12

GTACCACATCGGCATCGTGCTGGCCGCGCTGTGGGCCGCGGGCTCCCTCGGCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgct ... ttcattgtagGTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCACATCGGCATCGTGCTGGCCGCGCTGTGGGCCGCGGGCTCCCTCGGCTTCCGCCACTCCGTCCTCTTCCTCCTCGCCTTCCTCTACCTCTACATGgtacggtgctcttctgccgctgccgcccgcgcctctcgctgataagttgatgcgacttttttttttatcttttttgagctcctttacggcatatgcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctcgc