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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
ttaaccccaaataagtctaggtttcatct--tcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcct---gttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
   |  | ||  |  || |  |   |  |  |    |      ||||  |||| |   |  | ||||| | || ||||||  ||| |   ||| ||||||| ||||| | || || ||||||||||||||||||||||| || ||||| |||||||| |||||||||||||||||||||||||| ||| |||  |||||    ||
---aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtat-tattgtcacagtttcgtaatgtggatctttgtgtttccatttt-cagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
---ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
    |      ||| || |  |    | |  ||    | || |  |||    | | || |  | | |  | ||  |      | |  ||||    | |||||||||| || ||||||||||| ||||||||||| || || ||||| ||||| ||  |||| ||||| ||||||||||| |||||  |     | |||   ||
ctccttttatgaaagaatttaaaagatgaaattatgtttaatttatgtcagctgtagctt--tgttatgc-ctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
---ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
   ||       || || |  |    | |  ||  | | || |  |||  | | | || | ||    |   ||  |      | |  ||||    | |||||||||| || || |||||||| ||||||||||| || || ||||| ||||| ||  |||| ||||| ||||||||||| |||||  | |   | |||   ||
cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgc---ctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
-ttaaccccaaataagtctaggtttcatcttca-actaaaatattgtttttt---tttgcgtgctatcac--actctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
 | | |      | | | ||       | |  | |  | |||      ||||   |     |  ||| ||    | |  |  | | ||     ||    ||| | |||| | || || |||||||| || |||||||||||||| || || ||||||||||| || ||||| ||||| ||||| || ||| | |  || ||    ||
gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
-ttaaccccaaa-taagtcta-ggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
 | | |     | | | |||  | | | ||    |    || |      |   | | | |  ||     || |    || |||      || | || |||||||  | ||||| |||||||||||||||||||| || || || | |||||| ||  |||| ||||| ||||| |||||||||||  |||  || |||   ||
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgct-ttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 16
ttaaccccaaataagtctagg----tttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
| |   ||  ||   | || |    |   ||   |||||||   | |  ||   |  | ||  | |   | |||  |    |   | |  ||  | | ||||||| || ||||| |||||||| || |||||||||||||||||||||||||| || |||||||| || ||||| ||||| |||||  |     | ||    ||
taattgccggatgtctttaagaaaatggtattcacaactaatgaactaattcact--gagttgtgt-ggattctggttgc-tccctgcccttttcctctttcagAAATAAAGCTTGTGGATGTTCCTGAAATGAATTACACCTCTGAGGATCAGCCCTATCCTCGCGGTGAAATATGTGTCAGGGGTCCCGTTCTCTTCCAAGG

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttt-tgcgtgctatcacactctcata---atgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
      | | | || | | | |      | |||| |   | ||    || |  |  |||||     | | |   |   || ||  |    ||| | | |||||||  | ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||||||||| ||||| |||||| ||||  | |   | ||| | ||
----aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG

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|29679209|gb|CB675484.1|CB675484
EST:     TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG                         AGATTAAGCTAGTGGATGTCCCAGAAATGAAT-ACACCTCT
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCT
EST: gi|66919239|gb|CX106087.1|CX106087
EST:     TTGTGATGATAGGTTAA-TGGTCATGTTGGACCTCCAAATCCATCTTGTG                         AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
EST: gi|29679207|gb|CB675482.1|CB675482
EST:     TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG                         AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTG
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTG
EST: gi|58590451|gb|CF988759.1|CF988759
EST:     TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG                         AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
EST: gi|58595336|gb|CF993644.1|CF993644
EST:     TTGTGATGATGGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG                         AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
EST: gi|109974356|gb|DT806865.1|DT806865
EST:     TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG                         AGATTAAACTAGTGGATGTCCCAAAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
                                            ccatttttc  CT-rich tract
                          ataatgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA