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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatctttttccaaaataaacaaaaatgtgttgttgggaatgtagtaacttagtattgaggatttcttttattgcag

Basic information

species Oryza sativa
transcript LOC_Os08g34480.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 3
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatc--tttttccaaaataaacaaaaatgtgttgttggga-atgtagtaacttagtattgaggatttcttttattgcag
     ||| |||||||||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||  | ||||||||||||     | |||    || |||  |   |      ||   | |  |     |||| | |||    |||| ||  || |||
-----CGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaagatgctactaaattataagacatcaatgcttaattttg----tttccttatttacag

upper sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G121942_T03 (Zea mays), 5'ss of exon 3
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatc--tttttccaaaataaacaaaaatgtgttgttggga-atgtagtaacttagtattgaggatttcttttattgcag
|||||||| |||||||||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||  | ||||||||||||     | |||    || |||  |   |      ||   | |  |     |||| | |||    |||| ||  || |||
GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaagatgctactaaattataagacatcaatgcttaattttg----tttccttatttacag

upper sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatctttttccaaaataaacaaaaatgtgttgttgggaatgtagtaacttagtattgaggatttcttttatt-gcag
|||||||| || ||||||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||  | |||||||||||     || |      |  |  |||   ||||  ||  | | ||  |  |||    | |   |||   |||||  |||
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttt---tgtaacaaatcatgttactga-attatatgacattaccgcttaatgttttccttatttacag

upper sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatct------ttttccaaaataaacaaaaatgtgttgttgggaatgtagtaacttagtattgaggatttcttttattgcag
|| || || ||||| |||||||||||||| ||||||||||||||||| || ||||| || ||||| ||||| || ||||   |||||||||||| | |      || |    | |   ||  | |      ||| |||  || | |   | | ||||   ||| | |  | |   
GCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATTgtaagtatttttcactttttgtttggatttttcaggattccaaaattgtgaacttattgaa--aattttgaatgtttttgtgttag---

upper sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatctttttccaaaataaacaaaaatgtgt-tgttgggaatgtagtaact--tagtattgaggatttcttttattgcag---
|| || || ||||| ||||| |||||||| ||||||||||||||||| |||||||| || || || |||||||| |||| | |||||| ||| | | ||  |   |  |   ||||  | | | ||    |  | || |  ||  || | |   | |||  ||| | ||      
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttag-tgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag

upper sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagta-tatctttttccaaaataaacaaaaat-gtgttgttgggaa--tgtagtaacttagtattgaggatttcttttattgcag
|| || || ||||| || || || || || ||||||||||| ||||| |||||||| || || || ||||||||||||||| |||||||||||   | || ||  | | |        ||  | || ||   |   | |  |  |||||  |||| | ||| | |    ||||
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgg--gcag

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|88209922|gb|CI209771.1|CI209771
EST:     CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|86511433|gb|CI154066.1|CI154066
EST:     CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|86511143|gb|CI153776.1|CI153776
EST:     AGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: AGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|86855685|gb|CI269012.1|CI269012
EST:     CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|87020191|gb|CI261055.1|CI261055
EST:     CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCGTATATTGGGCA
genomic: CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|88210251|gb|CI210100.1|CI210100
EST:     CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTGAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|88213767|gb|CI213616.1|CI213616
EST:     CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|186893103|gb|FG124788.1|FG124788
EST:     CATCTCCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|88955817|gb|CI092106.1|CI092106
EST:     ATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGAAAGCTATGCATCCTATATTGGGCA
genomic: ATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|86526156|gb|CI166362.1|CI166362
EST:     CTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|86598009|gb|CI278399.1|CI278399
EST:     CTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT                         TGAATGGCCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: CTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
EST: gi|88240818|gb|CI238669.1|CI238669
EST:     ATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTTGGATCGATT                         TGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA
genomic: ATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGAC-TTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCA

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: 75 (upstream exon), 71 (downstream exon)
Score: 37

GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatat ... tttattgcagTGAATGGGCAGTAAACATCCAAAGGGATAGCTATGCATCCTATATTGGGCACTATCCAATGCTGGCATATTTTTCCATTGCTGAGAATGAATCAATTGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatctttttccaaaataaacaaaaatgtgttgttgggaatgtagtaacttagtattgaggatttcttttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG