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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaacacatgggttgtcatgtgcccttcagctggttctcagaaacaggcaactgtttattcttcgataaattcactacttattctactttgcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g34620.5
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34620.5 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 5
acaacacatgggttgtcatgtgccc-ttcagctggttctcagaaacagg--caactgtttattcttcg-ataaat-tcactacttattctactttgcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG
        | |  ||  |  |||     ||| |||   ||| |  | ||  |  |   |  ||||    || ||| |||||  | ||| || |||| | |||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||    |||| |||
----tctttagcatgcaacttgctagcccaggtggcagtcaaatcctggatccgcccctggttctcaatatcaatgtcactgttaatt-tattttgttggtgcagTAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG

upper sequence: LOC_Os01g34620.5 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 5
acaacacatgggttgtcatgtgcccttcagctggttctcagaaa-caggcaactgtttattcttcgataaattcactactt----attctactttgcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG
  |||||     ||| | |         | |   || | | |||  ||   | |  | || | |  ||   ||||||| |     | ||| ||     | |||||| ||||||| ||||||||||||||||| || || || |||||  | |||||||||||||| ||  |  | ||||| |||
--aacaccctcattggctt-cataaaataccaaattattaaaaaatagatgatttgtgatgcctgcatgt-ttcactaatcgaacactct-ctccatctctgcagCCACTGGCCCACATTTCCACAAATATTCATAAAGGGGGAGTTCATAGGGGGATCTGATATTATTCTCAACATGCACCAG
















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|218500313|gb|FG954965.1|FG954965
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTAAGTAGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCCAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|33688088|gb|CF316327.1|CF316327
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86501844|gb|CI144477.1|CI144477
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86510934|gb|CI153567.1|CI153567
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|58675402|gb|CK064089.1|CK064089
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|33662135|gb|CF293102.1|CF293102
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86825099|gb|CI358251.1|CI358251
EST:     TCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: TCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATC
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATC
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|38477159|gb|CF961292.1|CF961292
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86431345|gb|CI084956.1|CI084956
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC                         CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG

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: 67 (upstream exon), 70 (downstream exon)
Score: 37

ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcaactgtttattcttcgataaattcactacttattctactttgcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG
                                         ctttgctt  CT-rich tract
         tttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaacacatgggttgtcatgtgcccttcagctggttctcagaaacaggcaactgtttattcttcgataaattcactacttattctactttgcttgtgcagCAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA