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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacaagcacttgcttaattgcttattggtttttcatggatcgtatttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccccttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG

Basic information

species Oryza sativa
transcript LOC_Os02g06840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 5
gtaagacaagcacttgcttaattgcttattggtttttcatggatcgtatttatcaagtgactgtttctcctagaatcactgggaatgctat-ttcgcccccttatttattgtggtctaa----ctttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG
             |   |||||| ||| ||| | || |   |     ||  ||   ||||   ||  ||  ||  |  ||  ||  |||   ||  || || |||| |  ||||    |     ||| ||||||||||||||||||| ||||||||| | || |||||||||||||| ||||||||||| ||||||||| | ||||| || ||||||||||| |||||||| |
------------gtaagttaattccttgttgctcttgcgcaggagtgatacat---gtgaactttgttctgagttttgctcagacggctgggttttcctccatattcacagtggctacaatttttttgttcagGATCATGTTGAAGGGTACCTTGCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACG

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------gtaagacaagcacttgcttaattgcttattggtttttcatggatcgtatttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccccttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG
                                                   |  | |    |||||  ||||  |||  |    | |||||| ||  ||||||     |      |    || ||  |   | ||||| |       |     | | || || | |       ||||||||||||||||||||||||||| | | || |  || || |||||||||||||| || ||||||   || |||||||| ||||| ||| | || |||||||
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctc-tacttgaataatcacttgataagatatcatgg-tcacatttatttgaaggaaaaattaaataaaaaaaa-agaaatgcaacaagtttcaaacctctgttttgattt-------ttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagacaagcacttgcttaattgcttattggtttttcatggatcgtatttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccccttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG
                          ||||  ||||||     |  ||  | ||  |    || |   |    ||||  ||        || | |    || |||   ||       |||||   ||||| |||||||||||||||||||   |||| |||||||| || ||||| ||| |||| ||||||||   |||||||||||| || ||||| || || ||||
-------------------------gtatttttttttctcaagtt-taactctcgcgcttttggtgtcc---aaatccttga-------atattggtttctcattctctgct-----actttcaccagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 6
------gtaagacaagcacttgcttaa-ttgcttattggtttttcatggatcgt--atttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccc-cttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG
      ||     |    |||   | | ||||||  ||  || |  || ||  |  ||   || |  ||   | |    ||     | |   || | || || ||||| | | | | |  |  | |     |   ||||| ||||||||||| ||||| | ||| |||| ||| || |||| ||| |||||||| |||||| | |||||||||||||| || ||  | || |||||||
gtaatggttttgtatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataattataaagttaatttgccccacatgtctgtgttactgtg----tgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG

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|29682551|gb|CB678826.1|CB678826
EST:     ATAGAGCAATTGAAGCAGAGGACAGAAAACATGGTGACTTCATGAGAATT                         GATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTT
genomic: ATAGAGCAATTGAAGCAGAGGACAGAAAACATGGTGACTTCATGAGAATTgtaagacaag ... ctttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTT
EST: gi|29657303|gb|CB653578.1|CB653578
EST:     ATAGAGCAATTGAAGCAGAGGACAGAAAACATGGTGACTTCATGAGAATT                         GATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTT
genomic: ATAGAGCAATTGAAGCAGAGGACAGAAAACATGGTGACTTCATGAGAATTgtaagacaag ... ctttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcactgggaatgctatttcgcccccttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG
                                       gtctaac  putative branch site (score: 2)
                                             ctttattc  CT-rich tract
                           ttatttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacaagcacttgcttaattgcttattggtttttcatggatcgtatttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccccttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT