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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCCATGGGTATGCTGCTGTAAATCGTTTTGGTGCTTTGCGCAATGATCATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatcagcctcctttgttaacaactaagttgacttaaacactcagcctgacctatgtaataatattttacttgcaggattttaactgcagtagtaa...

Basic information

species Oryza sativa
transcript LOC_Os11g39220.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G099666_T01 (Zea mays), 5'ss of exon 3
TGGCCATGGGTATGCTGCTGTAAATCGTTTTGGTGCTTTGCGCAATGATCATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatcagcctcctttgttaacaactaagt--tgacttaaacactcagcctgacc---tatgtaataatattttacttgcaggattttaactgcagtagtaa
||||||||| ||||||||||||||||||||||| ||| |||||||||| ||||||||||| || || ||||| || || ||||| |||||||| ||||||||||  |||||| |||||||| || | | |  |  || |||      |||| |||||      ||    |   |||  | |    ||  | |||||   |     
TGGCCATGGCTATGCTGCTGTAAATCGTTTTGGAGCTCTGCGCAATGACCATGATATATTCCAAACGTTTGAGGGGGACAATACTGTTCTTCTGCAGCAGgtactgatcagcatcctttgt-aaaagccagctgatggcttgttt-ttcagactgacaatacttggggcatgttttctcctttctgaaataaactgagatca---

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G820287_T01 (Zea mays), 5'ss of exon 3
TGGCCATGGGTATGCTGCTGTAAATCGTTTTGGTGCT-TTGCGCAATGATCATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatcagcctcctttgttaacaactaagttgac--ttaaacactcagcctgacc-tatgtaata-atattttacttgcaggattttaactgcagtagtaa--------------------------------------------------------------------------
 |      |  | ||   ||     | |     ||||  ||   |  | |   || ||||| || |||||||| || || || || |||||||| ||||||||||  ||||||  |||| |   | ||   || |||    |      |||| |||||  ||| | |   | || ||   || |  |   | | | |||  | ||                                                                          
-GTATGCAGAGAAGCCTGTGGTGGCCATGGCTATGCTGCTGTAAATCGTTTTGGACATATTCCAAACATTTGAGGGGGACAACACTGTTCTTCTGCAGCAGgtacttatcagcacccttcg--gaaaagccagctgatggcttgtttttcagactgacgatatttgagggacatgttttctgaaataaactgagttcagaggaaagttgggatcagtttctaaaaatgctatgaattcacttctccttaaataacgtgcatcttttcatgctcttgtag

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G445791_T01 (Zea mays), 5'ss of exon 3
TGGCCATGGGTAT-GCTGCTGTAAATCGTTTTGGTGCTTTGCGCAATGATCATGATATATTTCAGACATTTGAAGGAGATAATACAGTTC--TTCTTCAGCAGgtaccaatcagcctcctttgttaacaactaagttgacttaaacactcagcctgacctatgtaataatattttacttgcaggattttaa-ctgcagtagtaa
     | |   |     | ||   | | | ||| ||   |||    |  |     |   ||  |  | |    |       ||||||     |   | |||   | |  |  |||||    ||   |   ||| | ||   ||||   |      ||| |||   | || |||| |   | |  |   |   || | | ||   
-AATGAAGAAAACCAACGATGAGGACCTTATTGCTGACGTGCATGTTCTTTCGTCTGGGTTGAAAGCCTACATAACTTCATATACAGCCAAGTCTATAAGCgtatgcagagaagcctgtggtggccatggctatgctgctgtaaatcgtt--ttggacatattcca-aacatttgagggggacaacactgttcttctgcag---

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G31390.1 (Glycine max), 5'ss of exon 3
TGGCCATGGGTATGCTGCTGTAAATCGTTTTGGTGCTTTGCGCAATGATCATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatcagcctcctttgttaacaactaagttgacttaaacactcagc--ctgaccta-tgtaataatattttacttgcaggattttaactgcagtagtaa
 |||||||| ||||||||||| ||||| ||||||  |||| | || |||||||| || ||||| |||||||||||||| || |||||||| ||||| |||||    | |     |||       ||| ||  |||  |   | |   |    ||   ||| | | | ||  |  |  |||     ||||||    |  |    
AGGCCATGGTTATGCTGCTGTTAATCGGTTTGGTATTTTGAGAAACGATCATGACATTTTTCAAACATTTGAAGGAGACAACACAGTTCTGCTTCAACAGgtttttagctaaagcctaaagcc-caattatattgcttctcatagataataactactctacttttacaacctggttgttgttatgttttaatcagataacc--

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0662g00010.t01 (Vitis vinifera), 5'ss of exon 3
TGGCCATGGGTATGCTGCTGTAAATCGTTTTGGTGCTTTGCGCAATGATCATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatcagcctcctttgttaacaactaagttgacttaaacactcagcctgacctatgtaataatattttacttgcaggattttaactgcagtagtaa-----
 |||||||| ||||||||||| ||||| ||||||   ||| | ||||||||||| |||||||| |||||||||||||| || || || ||| | || ||||| || |       || || |   ||   |   |    |  |   | |     | | ||     | |    | | || || || | |   | |  || ||     
AGGCCATGGTTATGCTGCTGTCAATCGGTTTGGTAGCTTGAGAAATGATCATGACATATTTCAAACATTTGAAGGAGACAACACTGTGCTTTTGCAACAGgttcccacttaatcccattctactcagacagccttctcttga---ttaaataaaac-attgggcacttagatgcatg-agaatataagtgggaagaggaaagggc

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|29666946|gb|CB663221.1|CB663221
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|33800672|gb|CF326206.1|CF326206
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29684385|gb|CB680660.1|CB680660
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29642868|gb|CB647875.1|CB647875
EST:     GGAGATAATACAGTTCTTTTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: GGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29669185|gb|CB665460.1|CB665460
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29638689|gb|CB643698.1|CB643698
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29636951|gb|CB641960.1|CB641960
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29624634|gb|CB629645.1|CB629645
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCCATGGGTATGCTGCTGTAAATCGTTTTGGTGCTTTGCGCAATGATCATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatcagcctcctttgttaacaactaagttgacttaaacactcagcctgacctatgtaataatattttacttgcaggattttaactgcagtagtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT