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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccctctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG

Basic information

species Oryza sativa
transcript LOC_Os12g34860.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
--ttgcatcaagcatatccaccaataattt--tttacatgtttatttttgtatataaattgccctctgacttttttcccttttcctttt--tctgctgttc-tacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
   |       |  | ||      |  |||  | ||||   || |||  | | ||||  | |    ||   |   |     |  ||     | |  ||||  |  ||||||| ||||| ||||| ||||||||||| ||||||||||  |  |||||||| ||||| ||||||||||||||||||||||| || || |||||||| |
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 7
---ttgcatcaagcatatccaccaataattttttacatgttt-atttttgtatataaattgccctc----------tgacttttttcccttttcctttttc--tgctgttc-tacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
   |    || |   | ||   |  | ||||  |  |   || |||||| |    |||| | | ||           || | |  || ||     ||| ||  |  ||||  |  ||||||| ||||| ||||||||||||||||| ||||||||||| |  |||||||||||||| ||||||||||||||||||||||||||||| |||||||| |
gtataatctcta-tgtttctgtctcttatttaatgtacacttcatttttttgagaaaatagtcttcatcttggtgtcgattatgctcactgacagtttatcactattgtttgtttagTTTCCTCCTTGTTACAAGGATATGAGTTTCTGGATCAATGATGCATTTACAGAGAACAACTTATGTGAGGTTGTCAGAGGAATTGCTGGTGATCTTGTTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 9
ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccctctgacttttttc--ccttttcctttttctgctg--ttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
       |  ||| |  |    | | | || |    | ||| ||| ||| | | | |  | | | ||| |     | || |  ||||| || |    | | |||| ||| ||||| |||||||| |||||||| ||||||||||||   || || || |||||| | ||||| ||||| |||||||| || || |||||||| |
---tgctattcattttgagtcttgaatcttgaggaatctatatttttatttcagt-ggacacagtcttgtgagagcattctaatttttgtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAATGAATCATTCACCGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTCG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccc---tctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
  | |  |  | ||    |||    |  |  ||   |  | | | ||  |  | ||  |    |   |  |||  |  |           |  |||||| |||| ||| ||||| |||||||| || ||||| ||||| | |||   ||| |||||||| ||||| ||||| ||||| |||||||||||||| |||||||| |
--gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 7
-----ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccct-ctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
     || ||   | ||||   || ||  |||| | || ||||        | | |||  | | ||  || ||  |      |  |  || |||    || | |||| ||| ||||| |||||||  |||||||||||||| |||||   ||| ||||| |||||||||||||||||||| |||||| ||||||||||| ||||  
attaattacacacaacataataactaaatatttat-acctgttagagcccct-tgtaaccttctctattggctgctagaaactgactattgtct----ttttgcagTATCCTCCTTGTTACAAGGGCATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTGTAAGAGGAGTTGCTGGAGATTTTGTCC

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 7
-----ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccct-ctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
     || ||   |  |||   || ||  |||| | || |||| |       || |||  | | ||  || ||  |      |  |  || |||    || | |||| ||| ||||| || ||||| |||||||||||||| |||||    || ||||| |||||||||||||||||||| |||||| |||||||||||||||| |
attacttacacacaatataataactaagtatttat-acctgtt-agagccccatgtaaccttctctattggctgctagaaactgactattgtct----ttttgcagTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACAGAAAACAATTTATGTGAGGTTGTTAGAGGAGTTGCTGGAGATCTTGTCG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv19s0027g01480.t01 (Vitis vinifera), 3'ss of exon 2
-----ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccct-ctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
     || ||   | ||||   || ||  |||| | || ||||         || |||  | | ||  || ||  |      |  |  |  |||    || | |||| ||| ||||| |||||||| | |||||||||||| |||||   ||| ||||| |||||||||||||| ||||| |||||| |||||||||||||||| |
attaattacacacaacataataactaaatatttat-acctgttagagccca-atgtaaccttctctattggctgctagaaactgactatcgtct----ttttgcagTATCCTCCTTGTTACAAGGACAAGAGTTTTTGGATTAATGAGTTGTTCACAGAAAACAATTTATGTGATGTTGTAAGAGGAGTTGCTGGAGATCTTGTCG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 8
-----ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccct-ctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
     || ||   | ||||   || ||  |||| | || ||||        | | |||  | | ||  || ||  |      |  |  |  |||    || | |||| ||| ||| | |||||||| |||||||||||||| |||||   ||| ||||| |||||||||||||||||| | |||||| ||||||||||        
attaattacacacaacataataactaaatatttat-acctgttagagcccct-tgtaaccttctctattggctgctagaaactgactatcgtct----ttttgcagTATCCTCCTCGTTACAAGGACATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTATAAGAGGAGTTGCTGGAGA--------

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|29629252|gb|CB634263.1|CB634263
EST:     AGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: AGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|58695333|gb|CK084020.1|CK084020
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88221899|gb|CI221855.1|CI221855
EST:     CCCAGTTTTCAGAAGGCAAACTTGGTGTCAAGTGTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: CCCAGTTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86493496|gb|CI136129.1|CI136129
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|24468878|gb|CA305827.1|CA305827
EST:     TTTTCAGAAGGCAAACTTGGCGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|29661307|gb|CB657582.1|CB657582
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88202077|gb|CI202432.1|CI202432
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86493622|gb|CI136255.1|CI136255
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|29662501|gb|CB658776.1|CB658776
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88223742|gb|CI223591.1|CI223591
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88832351|gb|CI019292.1|CI019292
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86501835|gb|CI144468.1|CI144468
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86541540|gb|CI181746.1|CI181746
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88991649|gb|CI019827.1|CI019827
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86499426|gb|CI142059.1|CI142059
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TGTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88961812|gb|CI096965.1|CI096965
EST:     CAAGTTTAAGCCATTCTCAGAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: CAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86434161|gb|CI094504.1|CI094504
EST:     GTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: GTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86502413|gb|CI145046.1|CI145046
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86423293|gb|CI060866.1|CI060866
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88248226|gb|CI248075.1|CI248075
EST:     AAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: AAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 45 (upstream exon), 66 (downstream exon)
Score: 36

TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatataaattgccctctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG
              ctctgac  putative branch site (score: 36)
            ccctctgacttttttc  CT-rich tract
                   actttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccctctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
-tgcatca
- - - - - - - - -accaata
- - - - - - - - - - - - - - - -acatgtt