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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG

Basic information

species Oryza sativa
transcript LOC_Os05g38400.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 5
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
                                                                       |  |  ||||    | |  ||   | || |  ||   || |  |||| | | ||  | |   | ||    |      |    |||| | | |||||||| |||||||||||||||||||||||||||| |||||||| ||||| || |||||||||||||||||||||||||||||||| || || |||||||||||||| || ||||
----------------------------------------------------------------------ttgttgtagcttcatttgc-ccttttcttaagaaacaaagca--tactacatgaaattcgaagatttgtctt-----ttcatcaatgtcta-cttttctgctggtccagGTGTTTTTTAAGGATGTAGCCGGTTGTGACGAAGCAAAACAAGAAATAATGGAGTTTGTGCATTTCCTTAAAAACCCTAAGAAGTATGAAGATTTGGGAG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
-----gttagttcattctcttctt------------ctgttctactttgaaacgactgtca-aatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgtt--gttaagttacaataaaaactgtataatgacaagct-tttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
     |  | ||| || ||||||             ||| |    ||||       | | | |  |||      ||         ||   | || || | |  |  || |  | |  ||  | |||  | |  | |   |  ||  |  ||| | |||  | | ||  | |||  |       | ||||  || || ||| | | |||||| ||||| ||||| |||||||| || ||||||||||| ||||||||||| || ||||| ||||  || ||||| ||||||||  | || |
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgc--tggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
-----gttagttcattctcttcttctgtt-------ctact-----ttgaaacgactgtca-aatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgtt--gttaagttacaataaaaactgtataatgacaagct-tttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
     |  | ||| || |||||| |   |       || ||     |||       | | | |  |||      ||         ||   | || || | |  |  || |  | |  ||  | |||  | |  | |   |  ||  |  ||| | |||  | | ||  | |||  |       | ||||  || || ||| | | |||||| ||||| ||||| |||||||| || ||||||||||| ||||||||||| || ||||| ||||| || ||||| ||||||||  | || |
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgc--tggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatg--cagtagctactg-cttaaacgttgttaagttac--aataaaaactgtat---aatgacaag-----------cttttctgttg------gtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
|||||   ||| |||| ||||  | | |  ||| | | |||     | |    | | |      |   || | | ||     ||||  |   | || | || |  ||   | |  || ||| |   |  | || ||| | ||   | || || |  ||   |  |||||             |||| ||||       || ||||| | |||||| ||||| |||||||||||||| || ||||||||||| ||||||||||| || ||||| ||||| || ||||| ||||||||  | || |
gttaggagatt-tctttttcttctat-caatgagatggctgctgttttttgtgtttgttttaatagcgtgttcccca---cttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
                                                                                       |||  |    |  | |  |||  | | |  |  | |  ||||   || ||| ||    |  | | |          | || | || | |||| | | ||| |||||||| ||||| ||||| || ||||| |||||||| ||||||||||| |||||||||||||| || |||||||||||||| || || |
---------------------------------------------------------------------------------------gttagagacttagagttttgcctttgtttttaatgatccgtttggaatttataaacttacttttgt----------tgttttcttcg-ccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttg---ttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
                                                                                || || | ||| | |         | |  | |  |||    |  |  |     | | | | | ||  | | |   || |||     |||  | || | |||| | | |||||| ||||| || || || || || ||||| |||||||| ||||| ||||||||||||||| |||| || ||||| |||||||| || ||||
-------------------------------------------------------------------------------gtcagc-atttcaatcagggtggagaagttg-aattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttg-ccagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTG----TGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG---------------
                                        ||||   |||  || |         |||| | | |||   | | ||         |  || || | | |  |  |  |  | ||||   |||      |||  | || ||  |  |   |   || | ||    ||||||| | ||| |||||||||||||| ||    |||||| || ||||||||||| |||||||||||||| ||||| ||||| || ||||| ||||| ||||| ||||               
----------------------------------------gtcagccatggcattt---------catttact-tcagattat-ctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcagcaaggataattgctt--ttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 5
gttagttcattctcttcttctgttc----tactttgaaacgactgtcaaatatgaaatatataca---tgcacattgattctcaagctctgctagttccacctatt----caataatgcagtagctactgcttaaacgttgttaa-gttacaataaaaactgtataatgacaagcttttctgt-tggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
||||| | | | | ||||| |||      |  ||||     | | |  |  ||  ||||| |  |   |  ||| | ||| | |    || || | || ||||||      ||| || |  |     ||   | |   || |||   |||  || |  | ||| |  | |     ||||     | || ||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||| ||||| || ||||| |||||||| || || ||||||||||| ||||
gttagctaactgt-ttcttttgtcaaaggtggtttgtctttagtttgcagcatccaatatttttacagtatacaataattattatatcctccttgctc-acctatggttataatcattcgattttctctctctgactattattattattatcattattattgtttgtttatctatttttggacctagtacagGTCTTTTTCAAAGATGTTGCTGGATGTGATGAAGCAAAGCAAGAAATCATGGAATTTGTTCACTTCCTCAAGAATCCTAAAAAATATGAAGAGTTGGGAG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ31204 (Selaginella moellendorffii), 3'ss of exon 6
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
                                                                                                         |   |||||||| ||||    |||  ||       || ||   ||  | |     |  |          | |||||   ||| || ||||| ||||||||||| ||||| ||| ||||  | ||||| ||||| || ||||| ||||||||||||||||| |||||  | || |
--------------------------------------------------------------------------------------------------------gtat-gtagctacagcttctttgtttctagcggttgatcaattgtgcctga-----aatt----------tgcagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCG

upper sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 5
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgtta-agttacaataaaaactgtataatgacaagcttttctgttggtc-cagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
                                                                                                                            | || | || ||||||  |       |     |  |||   |  |||    |  |||||   ||| || ||||| ||||||||||| ||||| ||| ||||  | ||||| ||||| || ||||| ||||||||||||||||| |||||  | || |
--------------------------------------------------------------------------------------------------------------------------gtatgtagctacagttactttttttctagcggtttatcaattgtgcctgaaatttgcagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCG

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|58682109|gb|CK070796.1|CK070796
EST:     CTCAGGTGACGAAGATGGACAAAAATTCCAAAAACAAG                         GTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATG
genomic: CTCAGGTGACGAAGATGGACAAAAATTCCAAAAACAAGgttagttcat ... gttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG
                                      cttttctgtt  CT-rich tract
           ttacaataaaaactgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA