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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG

Basic information

species Oryza sativa
transcript LOC_Os07g12530.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12530.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G031780_T02 (Zea mays), 3'ss of exon 5
-----gtatgct-ccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG
      |   || |  |   | | | |  |   ||||| ||| ||  || || ||| | || |||||  ||||  |  | |||  |  |   | |  ||| | |||   ||||| | ||||||||||||||| ||||||||||||||||||||||| ||||| ||||| |||||  ||||||||||||| ||||| ||  |||| ||| |||||||||
gtaagttgcactgctgtcacttcatcttgtatgatacaccat-taactgagttttttttcctttcataacctttgtagagcctttgttttaac-ttctgaaaaatgcaaaaaat-tacagGTTTGGAAGCTTAATTTCATGTGAATCCTTCCATGCTGATGTACATGCTGGAAACCTATGGTTGCTCCGTGATGGGCGAATTGGTTTTATTGATTTTG

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G38380.2 (Glycine max), 3'ss of exon 6
gtatgctccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgt-gcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG
                  | ||| ||   |  ||   ||||| |   ||   || || |  | | |  || ||     ||||      |||  |  |  ||  ||||||| ||||||||||||| ||| || ||||| |||  || ||||||||||| |||||||||||| | ||| | || |  ||||| | | || | |||||| | ||||
-----------------gtatgactctgaaattc---tattttgcagtt--agcaatcctatacttcttttaact---agaac---tttgtctatctcggtataaaatgttgcagGTTTGGAAGTTTGCTTGCATGTAAATTGTTTCATGCAGATGTACATGCAGGAAATCTGTGGCTTCTACATGATGGTCATATTCGGTTTCTTAACTTTG

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G38380.1 (Glycine max), 3'ss of exon 6
gtatgctccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgt-gcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG--
                  | ||| ||   |  ||   ||||| |   ||   || || |  | | |  || ||     ||||      |||  |  |  ||  ||||||| ||||||||||||| ||| || ||||| |||  || ||||||||||| |||||||||||| | ||| | || |  ||||| | | || | |||||| | ||||  
-----------------gtatgactctgaaattc---tattttgcagtt--agcaatcctatacttcttttaact---agaac---tttgtctatctcggtataaaatgttgcagGTTTGGAAGTTTGCTTGCATGTAAATTGTTTCATGCAGATGTACATGCAGGAAATCTGTGGCTTCTACATGATGGTCATATTCGGTTTCTTAACTTTGGT

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G36520.1 (Glycine max), 3'ss of exon 6
gtatgctccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggca-tgttgacatatgtgcaaaatgt-gcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG
                  | ||| |||  | || |||| ||   ||     |  ||| | || | |       ||||   || | | | |||  |  |  ||  ||||||| ||||||||||||| ||| || |||||||||| || ||||||||||| |||||||||||| | ||| | || || ||||| ||| |||| |||||||| || |
-----------------gtatgactccg-aaattatattttgcagt-----taacatcctttacttc------tccttttaacaagaactgtgtatctcggtataaaatgttgcagGTTTGGAAGTTTGCTTGCATGTGAATCTTTTCATGCAGATGTACATGCAGGAAATCTGTGGCTTCTACGTGATGGCCGTATTGGGTTTCTTGACTTCG

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgctccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG
          |  |  |||   | | || | || ||  |||  | |  |||| ||    |       ||  |    | || | |      |   ||| ||     ||  |||||||||||||||||  || | ||||||  ||||||||| ||||| ||||||||||| |||||| || | || ||||| ||  |||| |||||||||||||
---------gtaagatctttgaaattca-atattatg-attaagattgttctccctccta------aatgtagctgttagta-aaatgaatcttcatgtg-atgtaacttgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 3'ss of exon 7
gtatgctccatgcgtc--cttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG
||| |   ||  | |     ||   |||   |  |    | ||| | | ||| |    |   |      ||   |  || | ||     || |   |||   |      | ||||||||||| || ||| || | |||||| |||| ||||||||||| |||||||| ||||| |||||||| || ||||| ||  |||| |||||||||||||
gtaggactcaaacttggatctgcagttcataagctttcttgttttgatttttatttattggctaataacatcagaatcttataagttcaatctcttcattgatatgtt-tctgcagGTTTGGTAGTTTGCTTGCCTGTGAAACCTTTCATGCAGATGTTCATGCAGGCAATTTGTGGTTGCTACGTGATGGCCGCATTGGGTTTCTTGATTTTG

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|29615506|gb|CB620518.1|CB620518
EST:     TGCACTTAATGTCTG                         GTTTGGAAGCTTGATNTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
genomic: TGCACTTAATGTCTGgtatgctcca ... aaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
EST: gi|29677141|gb|CB673416.1|CB673416
EST:     TCTCTTGTTCCTGATCCTGAGCTGACTTTAGTCACTGCACTTAATGTCTG                         GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
genomic: TCTCTTGTTCCTGATCCTGAGCTGACTTTAGTCACTGCACTTAATGTCTGgtatgctcca ... aaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
EST: gi|29619071|gb|CB624083.1|CB624083
EST:     TCTCTTGTTCCTGATCCTGAGCTGACTTTAGTCACTGCACTTAATGTCTG                         GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
genomic: TCTCTTGTTCCTGATCCTGAGCTGACTTTAGTCACTGCACTTAATGTCTGgtatgctcca ... aaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
EST: gi|33796723|gb|CF324229.1|CF324229
EST:     TCTCTTGTTCCTGATCCTGAGCTGACTTTAGTCACTGCACTTAATGTCTG                         GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
genomic: TCTCTTGTTCCTGATCCTGAGCTGACTTTAGTCACTGCACTTAATGTCTGgtatgctcca ... aaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
EST: gi|29615297|gb|CB620309.1|CB620309
EST:     GACTTTAGTCACTGCACTTAATGTCTG                         GTTGGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
genomic: GACTTTAGTCACTGCACTTAATGTCTGgtatgctcca ... aaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
EST: gi|29615223|gb|CB620236.1|CB620236
EST:     GACTTTAGTCACTGCACTTAATGTCTG                         GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG
genomic: GACTTTAGTCACTGCACTTAATGTCTGgtatgctcca ... aaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG
                             tgttgac  putative branch site (score: 3)
      ttattcaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA