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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttcttgtagaacactaaaaggagtccttgcttagttatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
-----agtttcttgtagaacactaaaaggagtccttgcttagt-tatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
     | ||||   || ||   | ||   |    ||| || |  | ||||  |||      |||||     | |     | |||   ||| |||| ||     ||||||| ||| | ||||| || ||  | || ||||| |||||||||||||||||||| |||||||| ||| | ||||| ||||| |||||||| || || ||
atcatattttcccttataatgattaataaa---tttgtttggcctgtgctgcatg---agagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12
---agtttcttgtagaacactaaaaggagtccttgcttagttatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcccac---cagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
   | || |   || ||   | || | |    ||| ||     ||   |  || |||   |||    |   |       |  |||||| ||| |   ||    ||||||| ||| | ||||| || ||| | || ||||| |||||||||||||||||||| |||||||| ||| | ||||| ||||| |||||||| || || ||
tatatttgcccttaaaatgattaatgaa----ttgtttgaccgtgtgct--gcttgagagttttaacactgattttgataatatatttcttttttttcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
agtttcttgtagaacactaaaaggagtccttgcttagttatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttt-tctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
            ||   |   |||    |    ||| |  |  || |||  |    ||  || |    |        |  | |||||  | ||    |||||||| ||||| |||||||| ||  | || |||||||| ||||| ||||||||||| || || ||||| || ||||| ||||| ||  | || ||||||||
----------gtaatgttc--aggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
-----------agtttcttgtagaacactaaaaggagtccttgcttagttatgctt-tatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
           || || || | |     | ||   |    || |  |||| ||  | | |     |  || | ||    | |||    |||||    | |||        ||| || |||||||| ||||||||  | |||||||| || ||||||||||||||||| ||||| || ||||| |||||||| |||||||||||||| || ||
tttccattggtagcttttttttgg----tgaagcaacatttttccaagttttgtatatttattcaaaattattttctaaaccaatgtgatcatggaatgttc--------agGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
-----agtttcttgtagaacactaaaaggagtcc---ttgcttagttatgctttatgcctgatgttttctttatcaacaaa-acaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
     || || | || |     |  |     |     || | | ||||||     ||| |||  |  | ||   |||| || |  ||  |   ||||||        ||| || || || |||||||||||| | || |||||||| ||||| ||||||||||| ||||| || ||||| ||||| || || ||||| || || |||||
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgc-tgagatgatgttctccaactaatatgattgtgggtttttc--------agGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------agtttcttgtagaacact----aaaaggagtccttgcttagttatgctttatgcctgatgtt---ttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
                                                    || | ||||  | |    ||| |   || | ||||  ||    |||  || |    ||   | |||| |  |          | ||| | || |      |||| |||||  | || || |||||| | || ||||| ||||||||||||||||||||||| ||||| ||||| ||||| || ||  | || || ||||| ||
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------agtttcttgtagaacactaaaaggagtccttgcttagtt---atgct-ttatgcctgat-gttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
                                   ||    | |  |||  |   |    || |||  |  ||   ||||| |  ||  |||| |  | |||   || ||  |     ||  | ||| |||     |||| || ||  | || ||||||||| | || ||||| || ||||||||||||||||| || ||||| ||||| |||||||| ||  | ||||||||||| ||
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcc-tctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgtt--gcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 11
agtttcttgtagaacactaaaaggagtccttgcttagttatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcc-caccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
                                                     ||||  |    ||  |     ||    |  |||| ||        |||| |||||  | ||||| || |||||||||||||||||||||||||||||||||||||| || || ||  | ||||| ||||| |||||||| || || ||
---------------------------------------------------gtatgtccttccaattca-ggctcagcgctgattttatcgatggtttcagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 12
agtttcttgtagaacactaaaaggagtccttgcttagttatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcc-caccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
                                                     ||||  |    ||  |     |||   |  |||| ||        |||| |||||  | ||||| || |||||||||||||||||||||||||||||||||||||| || || ||  | ||||| ||||| |||||||| || || ||
---------------------------------------------------gtatgtccttccaattca-ggctcaacgctgattttatcgatggtttcagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

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|58692820|gb|CK081507.1|CK081507
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58611693|gb|CK039405.1|CK039405
EST:     TAACACATCCAACATGCCTGTGGCGGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58601223|gb|CK011751.1|CK011751
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTA
EST: gi|58659487|gb|CK048167.1|CK048167
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     TAACACATCCAACATGCCTGTGGGTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|29617005|gb|CB622017.1|CB622017
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|27578142|gb|CB000837.1|CB000837
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58594482|gb|CF992790.1|CF992790
EST:     TAACACATCCAACATGCCTGGGGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
   gcctgat  putative branch site (score: 4)
                                     tttttttctgcccacc  putative PPT
                tttatcaacaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttcttgtagaacactaaaaggagtccttgcttagttatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC