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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatctcctgttttcttcatcacacggatattttccaacttcggacgaactgaattgaacaaagtctacctgttcacttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g32610.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatctcctgttttcttcatcaca--------cggatattttccaacttcggacgaactgaattgaacaaagtct--acctgttcacttgcag-----------------------------
 ||||| |||||||||||||||||||| |||||||| ||||| ||| |||||||||| ||||||||||| || |||||||||| ||| ||||||||||||||||| ||||| || ||| | |||||||          ||  ||||| | |||  ||   ||   || ||  |||  ||  |  | |    ||   |                             
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA19G37570.2 (Glycine max), 5'ss of exon 14
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgt-----atctcctgttttcttca------tcacacggatattttccaac----ttcggacgaactgaattgaacaaagtctacctgttcacttgcag
 |||||||| ||||||||||| ||||| |||||||||||||| ||| | |||||| ||   ||||||||||| || ||||||| |||||||||| | |||||||||     | ||    | |  ||||      | |  |  | |||||||||     ||     |   ||| ||  |  ||   | | |    |  ||   
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtgcttatgcttagattttccaatacgattatattgctttgatttttatgaaagattctttaagatctga--

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA03G34890.1 (Glycine max), 5'ss of exon 14
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtat--ctcctgttttcttca------tcacacggatattttccaacttcggacgaactgaattgaacaaagtctacctgtt---cacttgcag---
||||||||| ||||||||||| ||||| |||||||||||||| ||| | |||||||||   ||||||||||| || ||||||| |||||||||  | |||||||||||  ||    | |  ||||      | |  |  ||||||||||  | ||     | ||   |||      |  |  | ||   ||   ||||   
TGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCGCCACAGgtttgtataactttgatatatttcagtgtgcttatgcttatattttcca-ttacgactatattgttctgatttttatgaaagtcttaggcatgagcaggaa

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA10G07610.1 (Glycine max), 5'ss of exon 15
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatctcctgttttcttcatcacacgg--atattttccaacttcggacgaactgaattgaacaaagtctacctgttca---cttgcag--------
||||||||| ||||||||||||||||| |||||||||||||| ||| ||||||||||    ||||||||||| ||||||| || ||| |||||||| |||||||||        | |  | ||| | |  |   ||| ||    |||   |        |||      | | ||  | ||||    ||            
TGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGCAACAGCCATGGATTAATTTAAATCCAGCACAGgtttgttgtatagctgtgatacatgatattgcagtatgtttatgcttaatagttgtattattattattattatattttttcagcatttatgaaacttgtg

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA13G21480.1 (Glycine max), 5'ss of exon 13
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatctcctgttttcttcatcacacggatattttccaacttcggacgaactgaattgaacaaagtctacctgttcacttgcag-------------
||||||||| ||||||||||| ||||| |||||||||||||| ||| ||||||||||    ||||||||||| ||||||  || ||| |||||||| |||||||||        | |  | ||| | |  |   | |    |      |       | |   |  |    ||    |    |||  |             
TGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGCAACAGCCATGGGTTAATTTAAATCCAGCACAGgtttgttgtatagctgtgatacatgatattgtagtatgtttatgcttaatagttctattattattattattattattgttattgttgttgctgttattat

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgt---ttgtatctcctgttttcttcatcacacggatattttccaac-ttcgga-------cgaactgaattgaacaaagt-ctacctgttcacttgcag---------------
|||||| || ||||| ||||| ||||| |||||||| || || ||| | ||||||||    |||||||||||||||||| |||  || ||||| ||||||||   ||  |         |     || | |  |||||| |    | || |||       |   ||  |||  | ||  | |||  | |   | | ||                
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaaacatctcaaataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 13
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatctcctgttttcttcatcacacggatattttccaacttcggacgaactgaattgaacaaagtctacctgttcacttgcag------------------
|||| |||||||||| ||||| ||  | || ||||||||| | ||| | ||||| ||    |||||||||||||| ||||||| ||| |||||||| ||||||||| |       ||   | ||   |  || ||  |  ||     || ||     ||||    | |  ||  | ||   ||| ||                  
TGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgtcttctgaagttatgtaatgcaagtgaaatcattgaa----agaagagagagattgt-tgatgattatatttttctttgaagggagatgatgcaattctt

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 5'ss of exon 13
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgt---ttgt-atctcct--------gttttcttcatca-cacggatattttccaacttcggacgaactgaattgaacaaagtctacctgttcacttgcag--
||||||||||||||| ||||| ||||| |||||||||||||| ||| | ||||| ||  |||| ||||||   || ||||    ||| ||||||||||||||   |||| ||  |||        | | |  |  | |  |   ||||||   |  |      |||||   |||   ||  |  |  || |   | | |   
TGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGCAAAGGCCTTGGAAACATTTAAATCCAGCTCAGgtagtttgtcattaccttgcagcaagctataattgttagtaaaaatatttggaagatatcagagaacttgtttg--taatattaagttgctatttggtacaa

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|29680443|gb|CB676718.1|CB676718
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29660723|gb|CB656998.1|CB656998
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29639477|gb|CB644486.1|CB644486
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29625152|gb|CB630163.1|CB630163
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29678550|gb|CB674825.1|CB674825
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|86833192|gb|CI334787.1|CI334787
EST:     GGGAGCTCATGACATTGCAACAACCATTGAGTACTTT-AATCCACCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCGTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29662085|gb|CB658360.1|CB658360
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29680716|gb|CB676991.1|CB676991
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|58689699|gb|CK078386.1|CK078386
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29665413|gb|CB661688.1|CB661688
EST:     GGGAGCTCATGACATTGCAACACCCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29664340|gb|CB660615.1|CB660615
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|33675051|gb|CF303290.1|CF303290
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAG
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTG-TTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAG
EST: gi|29630303|gb|CB635312.1|CB635312
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29631490|gb|CB636499.1|CB636499
EST:     TACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: TACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29675290|gb|CB671565.1|CB671565
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29672353|gb|CB668628.1|CB668628
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|29628356|gb|CB633367.1|CB633367
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
EST: gi|87015028|gb|CI273426.1|CI273426
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTTGTTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAG
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTG-TTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAG
EST: gi|58595275|gb|CF993583.1|CF993583
EST:     GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAG                         GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC
genomic: GGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatct ... tcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatctcctgttttcttcatcacacggatattttccaacttcggacgaactgaattgaacaaagtctacctgttcacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA