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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtgttataagttgtcagtgaaatcaagtgtatctgtatccaacagccactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA

Basic information

species Oryza sativa
transcript LOC_Os01g17180.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 3
aatgtgttataagttgtcagtgaaatcaagtgtatc-tgtatccaacagccactcatattttagagat------ctgacg-tcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
   | || |     | |   ||||||||| |||||  | |||        ||    | |||||    |      |||| | |    ||| ||| | || |||||||||||| || |||||||| |||||||| || ||||| || |||||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||| |||
---gagtcac----tttttctgaaatcaaatgtattatttattatttgatcatcatttttttacctgtgcgcttctgatgctttactctctaatt-ttatctttatagGGGATTTAAAGCTCTTAAACAAACTGTCAAGCTTTACTATAAGCTGGGGAAATACAAAGAAATGATGGATGCATATAGAGAGATGTTAACATACATAAAA

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 3
aatgtgttataagttgtcagtgaaatcaagtgtatctgt----atccaacagccactca--tattttag-agatctgacg-tcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
          |  || |  |||||||||  |||||   |    ||   ||   ||||    ||| || | |  ||||| | |    ||||||| | || |||||||||||| || |||||||| |||||||| || ||||| || |||||||| || || |||||||||||||||||||||||||| |||||||| |||||||| |||
-------gccactttttttgtgaaatcagatgtattatttattattttaccatcacttcgttatctttgcacttctgatgctttactctgtaa-tgttatctttatagGGGATTTAAAGCTCTTAAACAAACTGTCAAGCTTTACTATAAGCTGGGAAAATACAAAGAAATGATGGATGCCTATAGAGAGATGTTAACATACATAAAA

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 3
-aatgtgttataagttgtcagtgaaatcaagtgtatctgtatccaacagccactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
   |||  |  |   |   ||| | || | ||  |  |  || | ||||  |   | ||     |  | |  | |    | | || ||    | ||  |||||| || |||||||| || ||||| |||||||| |||||||  ||||| | ||| ||||| |||||||| ||||| |||||||||||||| ||||| || 
ttgtgtagtgcatagtaatagtaatattatgttaaaat-cattccacagtgataaaaatccattacgtattgcttttcatatttatcttacattttactagGGGATTTAAAGCTCTAAAGCAAACTGTGAAGCTCTATTATAGACTTGGAAGGTATAAAGAGATGATGGAAGCCTACAGGGAGATGTTGACTTACATTAAG

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 3
aatgtgttataagttgtcagtgaaatcaagtgt---atctgtatccaacagccactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
   ||  |  |   |   ||| | || | || |   |    |  |  ||||  |     |      |  | |  | |    | | || ||    | ||   ||||| || |||||||| |||||||| |||||||| |||||||  ||||| | ||| ||||| |||||||| |||||  ||||||||||||| ||||| |||
---gtagtgcatagtaatagtaatattatgtcttagaatcattcctcacagtgataataaaccattatgtattgcatttcatatttatcttacattttaccagGGGATTTAAAGCTCTAAAACAAACTGTGAAGCTTTATTATAGACTTGGAAGGTATAAAGAGATGATGGAAGCCTACCGGGAGATGTTGACTTACATTAAA

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 3
------aatgtgttataagttgtcagtgaaatca-agtgtatctgtatccaacagccactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
       ||||   | |   |   | |    | | | | | |||      |  ||  |||  |   ||    |  | |  |   |||||||      |||| |  ||||| || |||||||| ||||| || || ||||| ||||||   || || | ||| ||||| |||||||| ||||||||||||||||||||||| || || 
ctctttcatgtaccacatagtaatatttgtctgagaatctttctactgtgataagaaactactgcattttgcacttaattttcattctgta------ttctat-cagGGGATTTAAAGCTCTAAAACAGACTGTCAAGCTATATTATCGACTGGGAAGGTATAAAGAGATGATGGAAGCCTATAGGGAGATGTTGACATATATTAAG

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 3
aatgtgttataagttgtcagtgaaatcaagtgtatctgtatccaacagccactcatattttagagatctgacgtcagttctgtaactcttttctttat-agGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
 |      ||   ||| |  |   ||   || |||| |||          |    | ||| |    |       |  |||  |  |   |||  || | ||||||||||||||||| || || || |||||| | ||||||   || || || ||||||||||||||||| |||||||  |||||| | ||||| ||||| 
-aaagaagattcattgcctctactattctgtctatccgtagtatgtgtgaaagtctgtttgaagttttgttaaaccattcaatggcctattttcttgtcagGGGTTTCAAAGCTCTTAAGCAGACTGTGAAGATCTATTATCGTCTAGGTAAATACAAAGAAATGATGGAAGCCTATACAGAGATGCTTACATATATCAAG

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
aatgtgttataagttgtcagtgaaatcaagtgtatctgtatccaacagc-cactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
|||  ||| | | | |  | | | |     ||  | |  |    |   |  | | || | |||    | |         | | | | |    | ||   ||||| || |||||||| ||||||||||| ||||| ||||||  | | |||||||| ||||| |||||||| |||||||||| ||||||||| || || |||
aattagttttga-tggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 3
aatgtgttataagttgtcagtgaaatcaagtgtatctgtatccaacagccactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
                                                       ||    ||   |      ||  ||||  ||       |     ||||| ||||| ||| |||| || || |||||| || ||| |    | ||||  ||||| || |||||||| ||||||||||||||| |||| |||||||| 
------------------------------------------------------gtaaacgagcttttctctttcttttct-caaagaaacaccacgcagGGGATTCAAGGCTTTGAAGCAGACCGTGAAGGTGCATTTTCGATTGGGGACCTACAAGGAGATGATGGACGCCTATAGGGAGATGCTGACGTACATCAAG

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|6431605|gb|AU081257.1|AU081257
EST:     CTTGCTGGCTTCGATCAAGTAGTACGTATGGANCCTGAAAAGGCTGAATG                         GGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAA
genomic: CTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATGgtaagcctta ... ttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAA
EST: gi|6431604|gb|AU081256.1|AU081256
EST:     CTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG                         GGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAA
genomic: CTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATGgtaagcctta ... ttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAA
EST: gi|86532861|gb|CI173067.1|CI173067
EST:     CTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG                         GGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAA
genomic: CTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATGgtaagcctta ... ttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagccactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA
                                  ctgtaac  putative branch site (score: 3)
                                        ctcttttctttat  CT-rich tract
                                           ttttctttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtgttataagttgtcagtgaaatcaagtgtatctgtatccaacagccactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- tgtgtta
- - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - -gtgtatc
- - - - - - - - - - - - - - - - - - tgtatcc
- - - - - - - - - - - - - - - - - - - - - - -cagccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgta