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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaggagtctgatcatgtaatagcagttagattgtacttgtgtgctaattaatggagtataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGGAGATGCTGATGCCCAAGGACCCCAACGCCACCATCATCATGCTGGGCAC

Basic information

species Oryza sativa
transcript LOC_Os02g01340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G059083_T02 (Zea mays), 3'ss of exon 3
--------gtaagctaggagtctgatcatgtaatagcagtt------agattg-tac-ttgtgtgctaatta-----atggagtataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGGAGATGCTGATGCCCAAGGACCCCAACGCCACCATCATCATGCTGGGCAC
           ||||   | |     |||||   ||   ||      ||| |  ||  || | | ||||  |     ||  |   ||||  ||||||| ||||||| ||  | || ||||||||||| ||||||||||| ||||||||||| |||||||| ||||||||||| || |||||||||        
gtcagttgtctagctttaatttccgccatgtctcagttcttccatgcagactaatatattatatactaagcatatatatacatactaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG--------

upper sequence: LOC_Os02g01340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G059191_T01 (Zea mays), 3'ss of exon 3
----------------------------gtaagctaggagtctgatcatgtaatagcagttagattgtacttgtgtgctaattaatggagtata-atttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGGAGATGCTGATGCCCAAGGACCCCAACGCCACCATCATCATGCTGGGCAC
                            | |  | |  |  |       |||  ||| || | | |  |    | | ||   |  |    | |  ||  ||||||| |||| |||||  | || ||||||||||| ||||||||||| ||||||||||| |||||||| |||||||| || ||  ||||||||        
ttttagctaactaactattagttctagtgcattcaaacaccccctaagcgtagaagcggtcaaactaaaagaatct-ctctcttgtatcctgtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG--------

upper sequence: LOC_Os02g01340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 4
---------gtaagctaggagtctg--atcatgtaatagcagtt-agattgtacttgtgtgctaattaatggagtataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGGAGATGCTGATGCCCAAGGACCCCAACGCCACCATCATCATGCTGGGCAC
            | | | | |||||  ||       |  | ||| | | ||| |||  ||| |  | |     |  |  || ||||||| ||||||| |||   || |  |||||||| || || || || ||||| ||||| ||||| || |||||||| |||||||||||||||        
gtaagaaagaagaacaatgtgtctgtgatggatcgtttacggtttaaactgttctta-gtgtttgtgatgttcgggtttttcagGTGACTTGAAGCCGGGTGATGAAGCTAAGATCACTGGACCTGTTGGCAAGGAAATGCTTATGCCAAAAGACCCCAATGCCACCATCATCATG--------

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|38479097|gb|CF963230.1|CF963230
EST:     CACCAACGATAAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|25798321|gb|CA754282.1|CA754282
EST:     CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAAG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|33656206|gb|CF278820.1|CF278820
EST:     ACCAACGATCAGGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGA
genomic: ACCAACGATCAGGG-AGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGA
EST: gi|8956400|gb|BE230203.1|BE230203
EST:     CACCAACGATAAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|29676003|gb|CB672278.1|CB672278
EST:     CACCAACGATCAGGGAGAGATCGTCAAAGGAGTTTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAACG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|58588294|gb|CF986602.1|CF986602
EST:     CACCAACGATAAGGGAGAGATCGTCCAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGAT
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGAT
EST: gi|58662943|gb|CK051629.1|CK051629
EST:     CACCAACGATAAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|38480865|gb|CF964954.1|CF964954
EST:     GATCGTCAAAGGAGTCTG-TCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCGAGTGGGGAAGG
genomic: GATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|38477836|gb|CF961969.1|CF961969
EST:     CACCAACGATAAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|38476458|gb|CF960591.1|CF960591
EST:     CACCAACGATAAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|8956756|gb|BE230559.1|BE230559
EST:     CACCAACGATAAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|33662396|gb|CF293363.1|CF293363
EST:     CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGA
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGA
EST: gi|29658349|gb|CB654624.1|CB654624
EST:     CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
genomic: CACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGG
EST: gi|38480242|gb|CF964331.1|CF964331
EST:     ACCAACGATAAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACGTGCCTCT                         GTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAG
genomic: ACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAAC-TTCCTCTgtaagctagg ... tataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtaatagcagttagattgtacttgtgtgctaattaatggagtataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGGAGATGCTGATGCCCAAGGACCCCAACGCCACCATCATCATGCTGGGCAC
                                 taattaatggagtata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctaggagtctgatcatgtaatagcagttagattgtacttgtgtgctaattaatggagtataatttagGTGACCTGAAGCCTGGTTCGGACGTGAAGATCACGGGGCCAGTGGGGAAGGAGATGCTGATGCCCAAGGACCCCAACGCCACCATCATCATGCTGGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG