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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC

Basic information

species Oryza sativa
transcript LOC_Os04g44430.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G062024_T01 (Zea mays), 3'ss of exon 13
taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttct-------tttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
   |   | ||  |||    |       | || || | || | | |    ||    ||      | ||| |||| ||||        ||  || || |   ||| |||| || ||||| | ||||||||||||    || || |||  ||||||||||||  |||||||  | || |||||| |||||||||||||||| |||||||
---agtttacttttcacgctgttgaacagaagcattttttcagtgt----atttaaatgcatgcacctagttaacttctgcatatgcttcgtttttttggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G164743_T01 (Zea mays), 3'ss of exon 13
taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcat-cctgatatgcatatctaattaatttcttttgat-tgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
     | |     |     |    | |   | ||||      ||||  || |   | ||      | |||  ||| || |    || | || | ||| | |||| || ||||| | ||||||||||||    || || |||  ||||||||||||  |||||||  | || |||||| | |||||||||||||||||||| |
--gttaatttacctttgatgctgtgaaacaattataagcattttttcatcgtatttaatgcatgcacctagataacttatgcatatgtttttttactcgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCGATCCATATATTTGGTGATGTCC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G32670.1 (Glycine max), 3'ss of exon 13
-taaacagtgctggtcaatgggaac-ggagggagtatatattgatttttctcatcctgatatgcatat-ctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
  ||  | |     |   ||      |||  || | | | |    |  ||  |   ||  |    |   || |    |||  || || | || |   ||  |||  || || || |||||||| || | |||||| |||||||||||| ||||  |||| ||||||||||| |||||||  || ||||| ||||| ||||| |
agaactaatctaaattgttgttccttggaaagaatttctgtaacctgatcagaagttggaagttttgcactcaaagttttgcttggaattttct---tttcagGGTCCTGTGAATTATGTATGTCTACGTTGTGTTAAACCAAGTTTGAGGCCTCTATCTATGGCTATGTCTACTGTTGTTATTCATATCTTTGGCGATGTAC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G30370.1 (Glycine max), 3'ss of exon 13
-------------------------------------------------------------------------------------------taa--acagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttg--attgttgtaacttg-----tagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
                                                                                            ||  || ||| | | | ||      |   |  |  ||| ||||  |  || |  || |||| | ||   || || | | |||    ||| || ||| ||      ||||  || || || |||||||| || |||||||| |||||||||||| ||||  | || ||||||||||| |||||||| || ||||| ||||| ||||| |
gtaattcacttctctgtgaagaagatttcctcatgtttgccttattatagtaagacatgctaaactatatgtacttataatgttagtatttcaactactgtgtttgactattcctctgttagctgagtatcttgaaatccctaa--cttatattcttaatgaactattatgtttcagtattcttataattttctttttagGGTCCTGTGAATTATGTATGTCTCCATTGTGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTAC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G06880.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------------------taa--acagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttgat--tgttgtaacttg-----tagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
                                                                             ||  || ||| | |   ||             |  ||| ||||  || || |   | |||| | ||   ||||| | | |||   |  | || ||| ||      ||||  || || || |||||||| || |||||||| |||||||||||| ||||  | || ||||||||||| |||||||| || ||||| ||||| |||||||
gtaattcacttcctcatgtttacctttttatagtaagacatgctagactatataggtgcttatcatgttagtatttcaactactgtgtttgagtattcctttattaactgagtatcttgaagttcctaa--gttatattcttaatgaattattatatttcagtgatcttataattttctttttagGGTCCTGTGAATTATGTATGTCTCCATTGTGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTGC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G33680.1 (Glycine max), 3'ss of exon 10
taaacagtgctggtca-atgggaacggagggagtatatattgatttttctcatcctgatatgc---atatctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
| |        | | | ||    |||     | ||||  || | |||| |     | ||  |    |||| |  || ||    |   | | ||     ||| |||| || ||||| ||||| |  || | |||||||||||| |||||| ||||| | || |||||||| || |||||| |||||||| | |||||||||||||
ttattttcttggattatattcttacgttattaatatagtttcaatttttttggagtcattggtttaatatttggttgatgatatggtactatt----tttgcagGCTCCTGTAAATTATGTTTCTCTCCGTTGTGTAAAACCTAGTTTGAGGCCACTGTCTATGGCTATATCTACTGTTTCAATCCATGTCTTTGGTGATGTGC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G06660.1 (Glycine max), 3'ss of exon 13
taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatat-ctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC-----------------------------
                                      |    |  ||  |   ||| |    |   |||| |  || |||   ||| |     ||| | ||  || || || ||||||||  | | |||||| | |||||||||| ||||  |||| |||||||||||  ||||||| || ||||||||||  ||||| |                             
-------------------------------------gtaacctgatcggaagttgaaagttttgcactaaatgtttgcttgcaatttt-----cttttcgggtcctgtgaattatgtatgtttacgttgtgttataccaagTTTGAGGCCTCTATCTATGGCTATGTCTGCTGTTGCTATTCATATATTTGTAGATGTACCTTCCTCGCCTCTTGTTGGAGTTCTCCAG

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G22730.1 (Arabidopsis thaliana), 3'ss of exon 12
-taaacagtgctggtcaatgggaacg--gagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
 |||| |||         |   |||   ||||     | ||||| || || | ||    || ||| |||  ||  ||   ||| || || ||    | |  |||| || ||||||||||| ||  | |||||||| ||||||||||| || ||||||||||||||||| || || || ||||| || ||||| || ||||| |
gtaaagagtaaaaaatggtttaaacattgaggagtcttgtattg-ttgttgtaatgtaaat-tgcttattcaag-aacagcttgtgtttctt----ccttcagGCTCCTGTAAACTATGTGTGTTTGCATTGTGTGAAACCAAGTTTACGACCATTATCAATGGCTATATCCACCGTCGCAATTCACATATTCGGCGATGTTC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 10
-------taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
       ||  | || ||| |   |    |  |    | ||  |||     |   |||   |  |  | ||||  | |||    | ||  ||  |||  | | | |||  || || || ||||||||||| |||||||| |||||||||||||| ||  |||||||||||||||| ||||||||||| || || ||||||||||| |
agttgcttatgctgtactgat--gttattatagcacaaataagtatctgcataggtca--gtattcaggatattcacttaga--cattcaatgtttgcca-tcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC

upper sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv07s0205g00120.t01 (Vitis vinifera), 3'ss of exon 13
---taaacagt--gctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttgatt--gttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
   |||| | |  |||||| | |     | |    |||| || ||   |     |||| | || | || |||| |   ||  ||    ||     | |   ||| |||| ||||| || ||||| || || |||||||| | |||||||||| | |||||||| ||||| ||||||||||||||||| || || |||||||||||||
tactaaaaaattggctggttactttt--ctgttttagta-atgtta--tgggagcatc-taat-ttcaaatcttacccatcactaacaatacaactttgctttgcagGCTCCAGTTAATTATGTTTGTCTACATTGTGTTAGACCAAGTTTGAGACCATTATCTATGGCAATGTCAACTGTTGCAATACACATCTTTGGTGATGTGC

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|88674005|gb|CI728118.1|CI728118
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|88670910|gb|CI725026.1|CI725026
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|88689877|gb|CI731455.1|CI731455
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCACGTCTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|87004271|gb|CI296813.1|CI296813
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|29672653|gb|CB668928.1|CB668928
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|88674418|gb|CI727429.1|CI727429
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|58671072|gb|CK059758.1|CK059758
EST:     TTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: TTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|88667854|gb|CI722593.1|CI722593
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
EST: gi|88669990|gb|CI724106.1|CI724106
EST:     GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAG                         GCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA
genomic: GATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCA

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: 72 (upstream exon), 67 (downstream exon)
Score: 131

TCTTGGAGCAATATTTTGTTTTGGTGCCTTTTGTTTCAAGAGCCTTTATGGATTCATACCCTTCTTTTCAGTAGGAGAGCTTTTGGTCTTTGCAACTCAGgttggttact ... taacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcatcctgatatgcatatctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
                                          ttgtaac  putative branch site (score: 131)
                 atatctaattaatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC

- - - gtgctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgt