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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgacagaactgatgttacttgacttccctatatgcag

Basic information

species Oryza sativa
transcript LOC_Os09g06970.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G123807_T01 (Zea mays), 5'ss of exon 3
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgacagaactgatgttacttgacttccc-tatatgcag
 ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||| ||||| ||||||||||| ||| |   | | ||| |  ||  |||| |   |     |  |||||  |  ||||||| ||  || ||||||
ACGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTCTGGTCAGAGCTGTTCAAGAAACAGATTGACAATCTGAAAACAAATCATAGGgtgatgcagaaatacttcctgtctgtttttccttctcgttaaccactgacatctcttgactacctatacatgcag

upper sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgacaga-actgatgttacttgacttccctatatgcag
|||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||| ||||| ||| |   | |  || ||| || |||  |  |  ||  | | |||||  |  |||||||    || | ||||
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttt-tttccccttcttgttaaacactgacatctcttgactattgtacacgcag

upper sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA19G42850.1 (Glycine max), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattc--gtaccttat------tttgcgcttgtgacagaactgatgttacttgacttccctatatgcag-----------
||| || |  |||||||| || || ||||| || |||||||| || |||||||| ||||| ||||||||||||||||||||  | || || || ||||||||   || || | |  ||   | ||||||      | |     | |      |   ||  |  |||| |    | |||   |           
TCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAACTTGAAGACAAACCATAGGgt---gagttcagagctctgatcccttatgggtggtatatatatatatatatatatatagtttttgattaaggtgtatttggttctgttgtag

upper sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgacagaactgatgttacttgacttccctatatgcag---------------
  | || ||||| ||||| || |||||||| ||||||||||||||||| ||||| ||| | ||||||||||||||||| ||| | || || |||||  ||||||   |  |   |||  |||||      |  |      || ||||  | ||   ||  ||    | |    |               
AAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAATTTAAAGACAAATCACCGGgtaagataactgggattt-tacct------gaacaaagaccaaaactcttcttgtgtgtgttattcacagatggaatgtttctcttcag

upper sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaat-----gaatttaaaat---tcgtaccttattttgcgcttgtgacagaactgatgttacttgacttccctatatgcag
 || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| || |||||  | || || || || || || |      |||||| ||||   | | | |||  |||     | |||   |   | |  | |||| |||            
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggcttatgcttgtcttgtag--------

upper sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ20859 (Selaginella moellendorffii), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgac-agaactgatgttacttgacttccctatatgcag--------
 ||||| |  |||||  | ||||  ||||| || || ||||| || || ||| | ||| | ||||||||||||||||||||||| ||||| |||||  |||||   ||    ||| |  ||  || | | || ||     | |   ||| | ||  ||  ||    | | ||           
GCGATTCACAGATCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAATCTCAAAACAAATCACCGGgtacgcaaaaacaaactt-tagtttttctcgctctctcatccattgctggttttgttttcctcttttgtgtgataactcccag

upper sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ32385 (Selaginella moellendorffii), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgac-agaactgatgttacttgacttccctatatg-cag-------
 ||||| |  || ||  | ||||  ||||| || || ||||| || || ||| | ||| | ||||||||||||||||||||||| ||||| |||||| |||||   ||    ||| |  ||  || | | || ||     | |   ||| | ||  ||  ||    | | || ||        
GCGATTCACAGACCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAATCTCAAAACAAATCATCGGgtacgcaaaaacaaactt-tagtttttctcgctctctcatccatcgctggttttgttttcctcttttgtgtgacaactcccag

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|88340008|gb|CI650455.1|CI650455
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGT
EST: gi|58659704|gb|CK048384.1|CK048384
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|218488990|gb|FG968333.1|FG968333
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAGTCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367807|gb|CI570546.1|CI570546
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|8335138|gb|BE040122.1|BE040122
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCATGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367760|gb|CI570499.1|CI570499
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTC-GGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367809|gb|CI570548.1|CI570548
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTGT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88378526|gb|CI636473.1|CI636473
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCT
EST: gi|88330158|gb|CI658463.1|CI658463
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367786|gb|CI570525.1|CI570525
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAAGATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88569468|gb|CI660643.1|CI660643
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88371498|gb|CI602676.1|CI602676
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88832250|gb|CI017484.1|CI017484
EST:     GAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|58685585|gb|CK074272.1|CK074272
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367769|gb|CI570508.1|CI570508
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367796|gb|CI570535.1|CI570535
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGAGAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTCTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367759|gb|CI570498.1|CI570498
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88570451|gb|CI661824.1|CI661824
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|33813782|gb|CF332777.1|CF332777
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT
EST: gi|88367808|gb|CI570547.1|CI570547
EST:     GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGG                         GGAACATTTGTTCTTCAAGATAACCGTTTGCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCT

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), 50 (downstream exon)
Score: 25

TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatt ... ctatatgcagGGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCTATAGATCCATCTGTAGAGAGCATGGATGCAACTGACAATGACTCTGCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgacagaactgatgttacttgacttccctatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT