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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttatctactaccatttctgtgctataaaatataatgcaagctatcgccatgcagatttcctgatcatggttatgtatctattttacatgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG

Basic information

species Oryza sativa
transcript LOC_Os03g51690.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g51690.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G017087_T03 (Zea mays), 3'ss of exon 3
tagttatctactaccatttctgtgctataaaatata-atgcaagctatcgcc-atgcagatttcctgatcatgg-ttatgtatctattttacatgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG
   || | |  || | |   | || |  |   | |  || |    ||| |||  |||     | |||   |||  |||   | || ||      |  |||||||||| |||||||||||||||||| ||||| || ||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||||| ||||
---ttttatcatatcttcattttgttggatgttttgtatacggcatatagcctgtgcttccctactggatatgaattaaccaactcttcccatcggtgagcagGAGACTCAGAAGGTGGCACTGGCTGAGTCTACCGGGCTTGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCATCCG

upper sequence: LOC_Os03g51690.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G10430.1 (Glycine max), 3'ss of exon 4
---tagttatctactaccatttctgtgctataaaatataatgcaagctatcgccatgcagatttcctgatcatggttatgtatctattttacatgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG
    |   |   | |  || || |   | ||||| | |     | |   | |  ||  | |||||   |   |   ||  | ||    |      |   | ||||     ||||||||||| |||| || || || ||  ||||||  ||||| || || ||||||||||| |||||||||||| |||| ||||| || || |
gtgaaaccacacatttacaatttt---caataaattttgtcatatgtgtttgatatatatatttctaaaaattatgtacttctcatggtggtcactactgtagGAATCAGAGAAGGTGGCATTGGCTGAATCAACTGGTTTGGACCAAAAGCAAATAAATAACTGGTTCATAAACCAGAGGAAGAGGCATTGGAAACCATCTG

upper sequence: LOC_Os03g51690.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
-------------------------tagttatctactaccatttctgtgctataaaatataatgcaagctatcgccatgcagatt-------tcctgatcatggttatgt--------atctattttac-atgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG
                         | |  ||    |  |  ||    | |||      |   ||  || || ||  ||    ||       ||||  |||| | | | |        || |  ||     ||  |  |||||||  || |||  |   || ||| | || || ||||||||||  |||||||||||||||||||| || |||||| | |||||||||||||| ||    |
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgg-gcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: LOC_Os03g51690.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
-------------------------tagttatctactaccatttctgtgctataaaatataatgcaagctatcgccatgcagatt-------tcctgatcatggttatgt--------atctattttac-atgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG
                         | |  ||    |  |  ||    | |||      |   ||  || || ||  ||    ||       ||||  |||| | | | |        || |  ||  |  ||  |  |||||||  || |||  |   || ||| | || || || |||||||  |||||||||||||||||||| || |||||| | |||||||||||||| ||    |
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgg-gcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

upper sequence: LOC_Os03g51690.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
tagttatctactaccatttctgtgctataaaatataatgcaagctatcgccatgcagatttcctgatcatggttatgtatctattttacatgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG
                               || |  ||  || | ||        || ||  |  || | ||| | |  ||  ||| ||   ||| |||||||     ||| |  | || ||       || || || |||| |||||| || ||||||||||| ||||||||||| ||||| || ||||| || || |
-----------------------------gtatgttgtgatagttttcatt-----gaatttatattcttagttgtttggctggttt-ca---gGAACAGGAGA-----AAGCTAAC-CTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG

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|58682618|gb|CK071305.1|CK071305
EST:     AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCG                         GAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
genomic: AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCGgtaagattca ... tgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
EST: gi|27554491|gb|CA998391.1|CA998391
EST:     AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCG                         GAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
genomic: AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCGgtaagattca ... tgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
EST: gi|58669450|gb|CK058136.1|CK058136
EST:     AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCG                         GAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
genomic: AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCGgtaagattca ... tgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
EST: gi|27577130|gb|CA999824.1|CA999824
EST:     AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCG                         GAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
genomic: AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCGgtaagattca ... tgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
EST: gi|58682318|gb|CK071005.1|CK071005
EST:     AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCG                         GAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG
genomic: AACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCGgtaagattca ... tgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgccatgcagatttcctgatcatggttatgtatctattttacatgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG
               tcctgat  putative branch site (score: 3)
                           ttatgtatctatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttatctactaccatttctgtgctataaaatataatgcaagctatcgccatgcagatttcctgatcatggttatgtatctattttacatgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG