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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccgctatttctgttttcttagttcaatatgtaccatatcaaccatctcttccatttcttgtgcatagtttaaagacgtcaggtctgttactctgcactgatattgatctttgtgttaaactggcaaactgatcattgagccatgtgcttgaactcactgacctttttgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os07g29630.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g29630.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 4
gtaatccgctatttctgttttcttagttcaatatgtaccatatcaaccatctcttccatttcttgtgcatagtttaaagacgtcaggtctgttactctgcactgatattgatctttgtgttaaactggcaaactgatcattgagccatgtgcttgaact--cactgacctttttgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG
                                                                                          || |    |  |   | ||  |  |||| |  ||      || |  | | ||  |      ||  ||||  || |   || ||   ||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
------------------------------------------------------------------------------------------gtaatcacgtgcacttcttatttcttgt-tcgaagatttgaattatttagtg--ctgataactgaaactaacattttactgttcttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG

upper sequence: LOC_Os07g29630.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
gtaatccgctatttctgttttcttagttcaatatgtaccatatcaaccatctcttccatttcttgtgcatagtttaaagacgtcaggtctgttactctgcactgatattgatctttgtgttaaactggcaaactgatcattgagccatgtgcttgaactcactgacctttttgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG
                                                                         | ||| | ||||  |   | |  |||     | |  |||    |   | || |  |||| |  |  |      ||   ||     |||      |||  |   |  |||| || ||||| || ||||| || || ||||| |||||  ||||  |||| ||||||||||| || ||||| |||||||| || |||||||||||  |  
------------------------------------------------------------------------gtgaaatatgtca--ttgctaatgctgttggaacacagatggagggccttaaat--caaattctttctcagaaaata-actaaggttcat----atttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
















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|33682993|gb|CF311232.1|CF311232
EST:     CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAG
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAG
EST: gi|88210242|gb|CI210091.1|CI210091
EST:     CTCCAGAATTGGCTGCCACCATGCAAGAA--T--TAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
EST: gi|33683745|gb|CF311984.1|CF311984
EST:     CTCCAGAATTGGCTGCCACCATGCAAGCATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
EST: gi|88848803|gb|CI087325.1|CI087325
EST:     CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
EST: gi|33682994|gb|CF311233.1|CF311233
EST:     CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
EST: gi|58587083|gb|CF985391.1|CF985391
EST:     CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
EST: gi|87018162|gb|CI277744.1|CI277744
EST:     CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
EST: gi|86595612|gb|CI264709.1|CI264709
EST:     CTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
EST: gi|86495728|gb|CI138361.1|CI138361
EST:     CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAG                         GCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGAC

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), 52 (downstream exon)
Score: 22

TCTGTCAAAAAGTGCTGAAGTTATGAAAATCGTTAACAATCTAATGAAAGCTCCAGAATTGGCTGCCACCATGCAAGAATTTAGTAAAGAAATGACAAAGgtaatccgct ... tgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaaactgatcattgagccatgtgcttgaactcactgacctttttgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG
                                 cactgac  putative branch site (score: 22)
                                       cctttttgcactct  CT-rich tract
                                         ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatccgctatttctgttttcttagttcaatatgtaccatatcaaccatctcttccatttcttgtgcatagtttaaagacgtcaggtctgttactctgcactgatattgatctttgtgttaaactggcaaactgatcattgagccatgtgcttgaactcactgacctttttgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG