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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgaaagcaatattccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g20100.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 5
gtaagtttgaa----agcaatattccttgatctggtccatctggaatgtataca-aactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
|||||  | ||    ||||| |||   | || || |  || ||   |   ||   ||||||||||  ||||  | || ||||||  |||||||||||||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| ||||| ||||||||||| |||
gtaagaataaacaaaagcaacattttctcatgtgctgaatatgctttaggtaagcaactgacatatggtttcttttg-ctcaaattagGCTGATGAGATGGCTCAGATATTCAGGCAGAGAATAGCTCAGGCAGAGGCTATGGCTCGTGCTGACATGTTGAGATTCCAGCCAGAG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G04190.1 (Glycine max), 3'ss of exon 5
---------------gtaagtttga---aagcaatattccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
                ||| | | |   || | || |   ||    | |    | | ||| |   |   ||| ||||| |   ||  || | |    | |||| || ||||||||||||| |||||| ||||| ||||| |||||||| || ||||||||||| || ||| |||| ||||||||||||
catcacttacatgttttaaatctaattcaacccatttctgttagcattggaatttttgaaggagaatttactcacataat-ccttaacttttttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATAGCCCAAGCAGAAGCTATGGCTCGTGCAGACATGCTAAGGTTCCAGCCTGAG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 5
---------------gtaagtttgaaagcaat--att--ccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
                |    || ||  |  |  |||  | ||    |  ||  | | ||| |   |   ||    ||| |  ||  |||||    |||  ||| || ||||||||||||| |||||| ||||| || ||||||||||| || |||||||||||||||||| | ||||||||||| |||
tctatgtttttaatcatctacttcaacccttttcattagcattatcattatcatttttgaaagagaatgcacacttataattcttaatctgttgttaaa--gGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 5
---------------gtaagtttgaaagcaatat----tccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
                |    || ||  |  | |    || ||    |   |  | | ||| |   |   || |  ||| |  ||  |||||      | |||| || ||||||||||||| |||||| ||||| || ||||||||||| || |||||||||||||||||| | ||||||||||| |||
tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaaagagaatgcacagttatatttcttaatctgttgtt--atagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaa----gtttgaaagcaatattccttgatctggtccatctggaatgtatacaaactgacatactgttttct-ctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
||||     |||  |  ||| |   |||   ||  |   | |    | | |   ||   |  | ||  ||||| |||||||||    |||||| ||||||||||||| |||||| ||||| || || |||||||| || ||||||||||| || ||| |  | ||||| ||||||
gtaactctatttccattcaaaaaaactttccctattttcttt----tatgtctcaatc-atttgctactttctgctgtctcaa----gGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtaagtttgaaa---gcaatattccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
                 |||     | |   |   |  ||||  | ||  |  |  |  | ||  |  | | |      || ||  | ||||   |  |||||| || ||||||||||||| |||||||||||| |||||||||||||| || |||||||| || || ||| |||||||||| ||||||
ttctgttacttcacctataaaccacacatgtgtgttgctcctctacctatttgaaatccagtgatttaacaatacttggctcttaaccctgttcta--acagGCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S40_14V6.1 (Physcomitrella patens), 3'ss of exon 5
--------gtaagtttgaaagcaatattccttgatctggtccatctggaatgtatacaaactgacatactgttttc------tctgtct---caaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGC----CTGAG--
         | |  ||   | |   |||  |   |   || | |   |  | | |||  | |||  |     |||       || ||     ||   |||||||||||||||||| |||  |||||||| ||| | |||||||| ||||||   ||| | || ||    ||  || | ||||       ||  
tttctatcctgaaattttgatcgtcattaatattttcagttcgtggtgcttatttacttattgaggtgtgtatttaagccaatcggttcttgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG

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|14713903|gb|AU197855.1|AU197855
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|86546307|gb|CI186513.1|CI186513
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAGGCTTGTTTTTGAGTAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|86866733|gb|CI343547.1|CI343547
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTTAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|88974484|gb|CI022025.1|CI022025
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|88975584|gb|CI021666.1|CI021666
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCCAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|18388863|gb|BM422061.1|BM422061
EST:     GCCGACACCTGGTGTACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: GCCGACACCTGGTG-ACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|218483682|gb|FG943816.1|FG943816
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|88983198|gb|CI020762.1|CI020762
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCCAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|88219484|gb|CI219044.1|CI219044
EST:     TTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTGAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: TTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|29638067|gb|CB643076.1|CB643076
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|88218693|gb|CI218542.1|CI218542
EST:     TGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: TGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|13165466|gb|AU174263.1|AU174263
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|29662710|gb|CB658985.1|CB658985
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|29660922|gb|CB657197.1|CB657197
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|29645770|gb|CB650777.1|CB650777
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|87010736|gb|CI312428.1|CI312428
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|29660751|gb|CB657026.1|CB657026
EST:     AGTCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|3768542|gb|AU032569.1|AU032569
EST:     GCCGACACCTGGTGACATGATTCGCNATGCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCCAGGCAGAGGATAGCTCAAGTCNGAGG
genomic: GCCGACACCTGGTGACATGATTCGCAAT-CCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATT-CAGGCAGAGGATAGCTCAAG-CAGAGG
EST: gi|29638932|gb|CB643941.1|CB643941
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
EST: gi|218480258|gb|FG945869.1|FG945869
EST:     AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAG                         GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA
genomic: AGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCA

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: 71 (upstream exon), 74 (downstream exon)
Score: 66

AAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTGTTTTTGAGAAGgtaagtttga ... ctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG
                      aactgac  putative branch site (score: 66)
                                ctgttttctctgtctc  putative PPT
            aatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgaaagcaatattccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT