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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatcttatattttgcattccatcatatagctttactcttagcctcttagcaatgagaactgtctatatattgctgaataataaaataactcttta...

Basic information

species Oryza sativa
transcript LOC_Os07g45350.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g45350.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G871572_T01 (Zea mays), 5'ss of exon 10
ATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatcttatattttgcattccatcatatagctttactcttagcctcttagc--aatgagaactgtctatatattgctgaataataaaataactcttta
 |||| |||| ||   |||  |||||| |||||| || ||||| || |||||||||||||||||||||||||| || || || |||||||||||||||||||||||||  ||| |||| ||   ||| |     |||   |   |       |||   ||     || | | | |||| |    |  |   |||| ||    
TTGGTTCATCGGACACAGAGCCTAACAGTAAAAAAGACCAATTAGTGTTGGACATATGTGTCATATGCCTTGAGCAAGAGTACAATGCTGTTTTTGTGCCgtaagtattgtatgttttccagagcataaatgttcttcgttgagaatgaagcagctggatttcctctatttttctatttcctttttttttcataattcca--

upper sequence: LOC_Os07g45350.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G020574_T05 (Zea mays), 5'ss of exon 10
ATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatcttatattttgcattccatcatatagctttactcttagcctcttagcaatgagaactgtctatatattgctgaataataaa----ataactcttta
| ||||||||||| | |||  |||||| |||||| |||||||| || |||||||||||||||||||||||||| || || || |||||||||||||||||||||||||  ||| |||| ||    | | |  |   |   | ||        |||||   ||  | ||| ||| || ||   |  |       |||| ||   |
AAGGTACATCAGACGCAGAGCCTAACAGTAAAAAAGATCAATTAGTGTTGGACATATGTGTCATATGCCTTGAGCAAGAGTACAATGCTGTTTTTGTGCCgtaagtattgtatcttttccag---aacttgaatgctctttgttgagaatgaagcaacttgattt-tctctatttttctatttcctttttcccataattccaaa

upper sequence: LOC_Os07g45350.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA10G02920.1 (Glycine max), 5'ss of exon 10
-ATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatcttatattttgcattccatcatatagctttactcttagcctcttagcaatgagaactgt-ctatatattgctgaataataaaataactctt-ta
 |  |  |  ||| | ||     |     |||||||||||  ||  |    ||  | ||||| ||||||||||| ||||||||||||||||||||||| |||||||      ||    | |  |   |    |  | | |    ||  || ||  |||||   | | |  ||||| || ||    |   || |  || || ||
AAAAGGCCGACAGCT-TATCAGATGGTGCTAAAAAGGATCGCTTAATGCCAGATTTGTGTGTAATATGCCTTGAGCAGGAATATAATGCTGTTTTTGTTCCgtaagctatcaatcccatcctctttcttgcttgacataaaa--tattctgttgtcaatgcttagtctgttatatgtttctctgcatacaactggctgttata

upper sequence: LOC_Os07g45350.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA02G16860.1 (Glycine max), 5'ss of exon 10
ATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaag-tatc--ttatattttgcattccatcatatagctttactcttagcctcttagcaatgagaactgtctatatattgctgaata--ataaaataactcttta
|     |    |   ||     |     |||||||||||  ||  |    ||  | ||||| ||||||||||| ||||||||||||||||||||||| ||||||| ||||  |   ||  |   ||  ||  | ||| |  |  ||||| |  |||    |     |||  || | |   |||  ||  ||||||| | |     
AAAAGGCTGACGGCTTATCAGATGGTGTTAAAAAGGATCGCTTAATGCCAGATTTGTGTGTAATATGCCTTGAGCAGGAATATAATGCTGTTTTTGTTCCgtaagctatcaatcccatcctcttttttattctgtag-tcaatgcttagtcagttatatgtttct-ctgaataca-acaactggctactataaaatcagtagc--

upper sequence: LOC_Os07g45350.4 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 5'ss of exon 10
ATGGTACATCAGATGTAGATTC--TAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatcttatattttgcattccatcatatagctttactcttagcctcttagc--aatgagaactgtctatatattgctgaataataaaataactcttta
       || |||  | |||    ||| |  |||| |||   | |  |    ||  ||||||| || ||||| || |||||||| |||||||||||||| ||||||| |  | | |     | ||||||  |||     |||| || |   ||   |  | |    | |   |   | ||  |   | ||    |  |   || 
-AAAAGGATGAGA-ATGGATCAGATAATACGAAAAGGGACAGACTAATGCCTGATCTATGTGTGATCTGCCTAGAGCAGGAATACAATGCTGTTTTTGTCCCgtaagcacttca-acaacac-ttccattttattttggtactgtttgatgctggacctatttttcatttcttgcctcttcttttttcattgtgtgtcatattc

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|58603294|gb|CK013822.1|CK013822
EST:     GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCGTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST: gi|25797586|gb|CA753547.1|CA753547
EST:     GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST: gi|29684519|gb|CB680794.1|CB680794
EST:     GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST: gi|88839227|gb|CI000699.1|CI000699
EST:     TATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: TATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST: gi|88270100|gb|CI381398.1|CI381398
EST:     ACAGGAATATAATCCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: ACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST: gi|38472971|gb|CF957103.1|CF957103
EST:     GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST: gi|29637828|gb|CB642837.1|CB642837
EST:     GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST: gi|29680616|gb|CB676891.1|CB676891
EST:     GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC                         GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatcttatattttgcattccatcatatagctttactcttagcctcttagcaatgagaactgtctatatattgctgaataataaaataactcttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT