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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacatacataatatctttggtgattatttactcactcttcttaacctttgcgtatccatcttatccactgaaatgcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA

Basic information

species Oryza sativa
transcript LOC_Os03g03180.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G060564_T03 (Zea mays), 3'ss of exon 7
gtaaaca-tacataatatctttggtgattatttactca------ctctt-----cttaacctttgcgtatccatcttatc-cactgaaatgcatg----tgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA
||| | |   |||  | |  ||   |     ||||| |      |||||     |  |||| |  | ||||| |||| |  || ||||||  |||    ||||||| || |||||| | |||||||||||||| ||||| |||||| |||||||||| ||||||||||| ||  |||| |||||||| ||||||||||||||||
gtatataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaaataaatgcaaatgcagACGCAGCACAAAGTCGAAATGGACAAGAGGGATGGAAAGTTCAGCCCACAGCCTATGGCAGTGCCCCCGGTGCAACAAATGTCACGCATCGATCAGCCTA

upper sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G060564_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------------------------------gtaaaca-tacataatatctttggtgattatttactca------ctctt-----cttaacctttgcgtatccatcttatc-cactgaaatgcatg----tgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA
                                                                                                      ||| | |   |||  | |  ||   |     ||||| |      |||||     |  |||| |  | ||||| |||| |  || ||||||  |||    ||||||| || |||||| | |||||||||||||| ||||| |||||| |||||||||| ||||||||||| ||  |||| ||||||||                 
taaggccgcccttaactgtctttttgcaaatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagggtttgtgcatgtatgcaggtatataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaaATAAATGCAAATGCAGACGCAGCACAAAGTCGAAATGGACAAGAGGGATGGAAAGTTCAGCCCACAGCCTATGGCAGTGCCCCCGGTGCAACAAATGTCA----------------

upper sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G060564_T02 (Zea mays), 3'ss of exon 6
--------gtaaacatacataatatctttggtgattatttactcactcttcttaacctttgcgtatccatcttatc-cactgaaatgcatg----tgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA
         |         |   | | ||  |||| |         |   |  |||| |  | ||||| |||| |  || ||||||  |||    ||||||| || |||||| | |||||||||||||| ||||| |||||| |||||||||| ||||||||||| ||  |||| |||||||| ||||||||||||||||
ataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaaataaatgcaaatgcagACGCAGCACAAAGTCGAAATGGACAAGAGGGATGGAAAGTTCAGCCCACAGCCTATGGCAGTGCCCCCGGTGCAACAAATGTCACGCATCGATCAGCCTA

upper sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G01990.3 (Glycine max), 3'ss of exon 6
gtaaacatacataatatctttggtgattatttactcactcttcttaacctttgcgtatccatcttatccactgaaatgcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCC---ATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA
||||   |   ||||   ||  |  ||  || |   |       ||  | |      |    ||||| ||   || |   | ||||||| || ||||| ||||| ||||||||| |||| ||||| || || || || ||    |||||||||||||| |||||||| ||||| ||||| ||||| |   
gtaagtttgtttaattatttctgaaatggttaatcaatatggtgtatgcatgataattatcacttatgca---aattttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAACCAGCAATGGCAGTGCCTCCTATGCAGCAGATGTCACGCATTGATCAAC---

upper sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G23470.3 (Arabidopsis thaliana), 3'ss of exon 7
--gtaaacatacataatatctttggtgattattta---ctcactcttcttaacctttgcgtatccatcttatccactgaaatgcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA
     | ||   || ||||| |        |||     ||| |  | |||||    | |  |   |   ||    ||  ||| | | || |||| |||||||| || |||||||||||||| || || |||||||| |||||||| ||||||||||||||    ||||||||||| ||  | |||||  | |
gtacgagcagtgatgatatcatatcaacccattccaatctctccttacttaaatcctac--acttacggtaatatctataatacttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAGCCAATGGCAGTGCCTCCGGCTCAGCAAATGTCACGGTTTGATCAAGCCA

upper sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv02s0025g00130.t01 (Vitis vinifera), 3'ss of exon 7
gtaaaca-----tacataatatctttggtgattatttac--tcactcttcttaacctttgcgtatccatcttatccactgaaatgcatgtg--------cagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA
|||| ||     ||||  | |    ||   || |   ||  |  || |   |||   |  |||   ||   | |  |||||  | | ||||        |||||||||||||| ||||||||||||||| ||||||| | ||| || ||||| ||||||||  | || ||  ||||||| ||||| ||||| ||||||||  
gtaagcaagagctacaacaaacacatgcaaatgagaaaccgtatctatatctaaatatcacgt-cacactatgttaactgatgttcttgtggagtattgcagACCCAACACAAGATTGAAATGGACAAGCGAGATGGCATGTTTGGACCACAACCCATGGCCATACCCCCTTTGCAGCAGATGTCACGCATTGATCAGCCAT

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|15847358|gb|BI795634.1|BI795634
EST:     CTCGTTTTGCCCCTGTATTGCAG                         ACCC-ACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACA
genomic: CTCGGTTTGCGCCTGTA-TGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACA
EST: gi|29656759|gb|CB653034.1|CB653034
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|88840715|gb|CI080169.1|CI080169
EST:     CTACTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTACTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|88832654|gb|CI008250.1|CI008250
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACGAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|25797080|gb|CA753041.1|CA753041
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|58592334|gb|CF990642.1|CF990642
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|88843869|gb|CI011127.1|CI011127
EST:     TGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: TGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|88835467|gb|CI005157.1|CI005157
EST:     CGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|86259413|gb|CI008090.1|CI008090
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|29623019|gb|CB628030.1|CB628030
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|325493801|gb|JG458325.1|JG458325
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|87008224|gb|CI299192.1|CI299192
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|86527924|gb|CI168130.1|CI168130
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
EST: gi|88994723|gb|CI036304.1|CI036304
EST:     CTGCTCGGTTTGCGCCTGTATGCAG                         ACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG
genomic: CTGCTCGGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAG

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: 22 (upstream exon), 67 (downstream exon)
Score: 19

GGTTTGCGCCTGTATGCAGgtaaacatac ... gcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcactcttcttaacctttgcgtatccatcttatccactgaaatgcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA
        ttcttaa  TA-rich tract