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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttatcttgctgtcttctgaatgtctgataactttccttgtgacagctgatcaatatttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG

Basic information

species Oryza sativa
transcript LOC_Os08g44530.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 11
--------------gtagttatcttgctgtcttctgaatgtctgataactttccttgtgacagc-tgatcaatatttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG
              | |  |||| | || || || || |   |  |  |||  ||   |      |||| |    |||||   |   ||| |  || |||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| || ||||||||||||
tgcatgtgtgcctggcaactatcctcctttcatcagattagttatt--cttcactacagttgatgtgataacctcttaaccaatgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 11
-gtagttatcttgctgt-cttctgaatgtctgataactt------tccttgtgacagctgat-caata----tttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG
     | |||| | ||  | | ||  || |   || | |      || |    |||||||||   |||     |||||  ||   ||| |  || |||||||||| ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |||||||| || ||||||||||||
taccttgatctagatgcacgtgtgcctggccactaccctggttattcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
--------------gtagttatcttgct---gtcttctgaatgtctgataactttccttgtgacagctgatcaatatttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG
              | |  | ||||  |   |  || |||||   | |||| |   | | ||   | ||    || |  | | | |  ||       ||| |||||   |||  |  |||| ||||| |||||||| ||||| |||||||||||||| || ||||| || |||||||||||||||
tatttgtagaaactgaaaatgtctttttcaagctttatgaat-cataataa-tgaacctatgctggatggc--atttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------gtagttatcttgctgtcttctgaatgtctgataactttccttgtgacagctgatcaatatt--taacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG
           ||||| | ||   | | ||       | ||   |  | |      ||| || ||  | | |   ||  |||    |        | ||||| |||||  | ||||| ||||| || || ||||| || ||||| || |||||||| ||||||||||| |||||||| |||
ttatgcttatggtagtgacctaaatctttttatctactttgtccatatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 11
gta-gttatcttgc---tgtcttctgaa--tgtctgata---actttccttgtgacagctgat-caatatttaacttgta--ttcaaacatcact--acagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG
 || ||| ||||     | | || ||||  ||  | | |   | |  | ||||  ||  ||||  ||| ||     || |  || |  | | |     |||||   |||  || |||| ||||| || ||||| ||||| |||||||||| |||||| |||||||| |||||||||||||| 
-tatgttctcttagacatattttatgaacctgcttaacactgagtacctttgtttcatttgatgtaatgttacttatggaattttattccttatgtggcagGATGTTGCTTTGTTGACTGATGGTAGGTTTTCAGGAGGTTCACATGGATATGTTGTTGGCCACATATGTCCTGAAGCACAT

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|86413805|gb|CI068012.1|CI068012
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGCGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|58586955|gb|CF985263.1|CF985263
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|88830002|gb|CI074674.1|CI074674
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|8858265|gb|AU095583.1|AU095583
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTNCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|86255894|gb|CI068343.1|CI068343
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|88965683|gb|CI006589.1|CI006589
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|218478481|gb|FG953986.1|FG953986
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|88309122|gb|CI654741.1|CI654741
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|88971557|gb|CI017871.1|CI017871
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|86823618|gb|CI258691.1|CI258691
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|86428510|gb|CI075191.1|CI075191
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|86537187|gb|CI177393.1|CI177393
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|89180557|gb|CI044836.1|CI044836
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|88848058|gb|CI086580.1|CI086580
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|88960472|gb|CI006433.1|CI006433
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|5038803|gb|AU070913.1|AU070913
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
EST: gi|86488131|gb|CI130764.1|CI130764
EST:     CTGAAATGCTGACTCCAACTAGTGCAATAAT-GGTGCTGGTCTTGGGAAG                         GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT
genomic: CTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTT

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: 74 (upstream exon), 70 (downstream exon)
Score: 44

GAAGGTAGTAGTGATACGAGGAGAAGGACCGAAAGGTGGACCAGGGATGCCTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGAAGgtagttatct ... atcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttccttgtgacagctgatcaatatttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG
                          atttaac  putative branch site (score: 44)
                       aatatttaacttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttatcttgctgtcttctgaatgtctgataactttccttgtgacagctgatcaatatttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC