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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGTTAGCAATTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgccatgcatttcttgtcgcatgccttagaacttttatgttgctgtcatcacatcaattagtaactgggttctgttcatggttacatttccgca...

Basic information

species Oryza sativa
transcript LOC_Os04g58750.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
AAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgccatgcatttcttgtcgcat---gcctta-gaacttttatgttgctgtcatcacatcaattagtaactgggttctgttcatggttacatttccgca
 ||||| |||| ||||||||| |||||||| ||||| || ||||||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| |  || |    | ||    |   || |||  ||    | ||      | |||   |   ||    ||  ||   |    ||| |  |||  |    
-AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagtt-ctttgaaaacatagttatgtttagcattacaaaacaatttgcattcataatc-tgttgcttgactacaaggaattaaggatgatgccatgacat--

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G37870.1 (Glycine max), 5'ss of exon 5
AAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagt---tgccatgcatttcttgtcgcatgccttag--aacttttatgttgctgtcatcacatcaattagtaactgggttctgttcatggttacatttccgca
 || ||   || | ||||||| ||||| || |||||||| || || || |||||||||||||| ||||||||||| ||  |  | |||||| | ||||||||| |||   |  |  ||| ||  |   |  |||||     | ||||    ||    |  |    |   ||        |  |||  || ||   ||| |   |  
-AGATTGATAAATCTGCTTGGATGTTGTTGTGAAGGTGAAGAAAGGTTACTTGTTGCAGAATATATGCCCAATGATACTTTGACAAAGCATTTATTCCATTgtaagtgcataactagcaattaattcagtttgcctgcattagctttggcatt----tacttgtttgggttctaggtcagactcttatcctgaacacaatctggt-

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G01730.2 (Glycine max), 5'ss of exon 4
AAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagt-------tgccatgcatttcttgtcgcatgccttagaacttttatgttgctgtcatcacatcaattagtaactgggttctgttca-tggttacatttccgca
 || ||   || | ||||||| ||||| || |||||||| || || || |||||||||||||| ||||||||||| ||  | || |||||| | ||||||||| |||       || ||   | |||   | ||  || ||||   |   || |   |||    |  |  |     ||||    |||   || ||  |           
-AGATTGATAAATCTGCTTGGATGTTGTTGTGAAGGTGAAGAAAGGTTACTTGTTGCAGAATATATGCCCAATGATACTTTGGCAAAGCATTTATTCCATTgtaagtgcataactgacaattaattcagtttgccagcattagctttgccatttacttgtttgtatttttaaatcaaactcttatctaaccagtgactgag--------

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G01300.2 (Glycine max), 5'ss of exon 4
AAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagt-tgccatgcatttcttgtcgcatgccttagaacttttatgtt--gctgtcatcacatcaattagtaactgggttctgttcatggttacatttccgca
 ||||| |||| ||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||||||| ||||| || ||||| ||||| |||||| ||    || |  ||   || |   || | |||    ||  |  |     ||  ||  | | ||||  |||     |   ||| | ||||   || ||   
-AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGGGAGGAGAGGTTGCTTGTGGCAGAATATATGCCCAATGAAACACTTGCAAAGCACCTTTTTCATTgtaagagctccttttatgcattttttaatcctttaagtgttgaacatctgattggtatgtcttaaatt--taataatatgtagtttacggttttgttgcctt-

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA07G07850.2 (Glycine max), 5'ss of exon 4
AAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgag-----ttgccatgcatttcttgtcgcatgccttagaacttttatgttgctgtcatcacatcaattagtaactgggttctgttcatggttacatttccgca
 ||||| |||| ||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||||||| ||||| || ||||| ||||| |||||| ||      |   |||||||| || |   || ||||  |    | |   |    |||  |  ||  | | |   ||| ||  | |  || | |  ||| |   
-AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATATGCCCAATGAAACACTTGCAAAGCACCTTTTTCATTgtaagagctccttttatgcatttttttt---attcctttaagtgctgaacatctgatcactatgtct-taaatttatggtttacggttttgttgatttttgctt-

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G00710.1 (Arabidopsis thaliana), 5'ss of exon 4
AAGGTTAGCAATTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgccatgcatttct-tgtcgcatgcc--ttagaacttttatgttgctgtcatcacatcaattagtaactgggtt--ctgttcatggttacatttccgca
|   |   |||||| || || ||||||||||||||||||||||| || ||||| ||||| |  ||||| ||||| |||||||| || || ||||| || ||||||   |  |     | | | | || |  |  |||  | | ||    ||||    |   |     | ||  ||  ||   || || ||| |   |        
AGAATGGCCAATTTACTCGGATGTTGCTGCGAAGGTGACGAGAGGTTACTTGTAGCAGAGTTTATGCCTAATGAAACACTAGCCAAACACCTTTTTCACTgtgagaatcatttttcctatatatagcctttcatttaataatcttgccatgctagtcttggaagttatggtgtctaagtgtactttttatgctactag-------

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 5'ss of exon 5
AAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc-atgcatttcttgtcgcatgccttagaacttttatgttgctgtcatcacatcaattagtaactgggttctgttcatggttacatttccgca-
 || || |||| ||||||||| ||||| |  ||||| || ||||| || ||||| |||||||  ||||||||||||||||| || ||||| || || |||||| |||| |  |  |||      ||   || | | | |  | |   ||    |     || || ||| |   |        |  ||  ||    | |   | 
-AGATTGGCAAATTTGCTTGGTTGTTGTTCTGAAGGAGATGAGAGGTTACTTGTCGCAGAATTTATGCCCAATGACACACTTGCAAAGCACCTGTTTCATTgtaagtttcttagacatgcaacatctggtgaccttgca--tatgctttagcatttgtgcaacatttattttatttaagaaatctatatttgggatactcaat

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 5'ss of exon 3
AAGGTTAGC-AATTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagt---------tgccatgcatt--tcttgtcgcatgccttagaacttttatgttgc-tgtcatca--catcaattagtaactgggttctgttc--atggttacatttccgca------------------------------------------------------------------------
 || || |  |||||| | ||||  ||||| || ||||| ||| |||| |||||||| |||||||||||||||||||| ||  | |  ||| | || || |||  ||         ||   ||| |   | || |  | |   |     |  ||| ||||| | |||     | |  ||     || | |   | | |  ||  ||||  ||  |                                                                          
-AGATTGGTGAATTTGATCGGCTACTGCTGTGAGGGTGATGAGCGATTACTTGTTGCGGAATACATGCCCAATGACACTCTTTCTAGACATTTATTTCACTgtaggtgctctttcttgtagtgcgtccgttttttttcttttttcttttcacttaagttgcatatcacagatccttcatagaagacggagcattatcccaatctttacggttgagttgaagagcgcaattttatcgtttcggctttccgtaaagatggttaaggtttgttgatttttgaaaatgcacag

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|33794016|gb|CF322898.1|CF322898
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
EST: gi|33675914|gb|CF304153.1|CF304153
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
EST: gi|29624788|gb|CB629799.1|CB629799
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC
EST: gi|58669011|gb|CK057697.1|CK057697
EST:     TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATT                         GGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTAGTTCTCTATC
genomic: TGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgcc ... gatttcccagGGGAGGCGCAAGCAATGAAATGGCCCATGAGATTAAGAGTTGTTCTCTATC