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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccataactccatgccaatgttcttgctattttcttgtataaagccctatttgtccaatttgtttagttgtttactctccttatgcttgcatgacatgacatgacag

Basic information

species Oryza sativa
transcript LOC_Os01g68770.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G103812_T02 (Zea mays), 5'ss of exon 5
TTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccataactccatgccaatgttcttgctattttcttgtataaagccctatttgtccaatttgtttagttgtttactctccttatgcttgcatgacatgacatgacag
||||||||||||||||||||| ||||| ||||| ||||||||| | |||||||||||||| |||||||||||||| || |||||||| |||||||||||||||||| |||  || ||||  ||  |  || | | ||        |  | | |  || ||||| ||| |||     || || |   | ||||||||                
TTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcatg-ctacatgataagttctttcccactta-------atgggcttgattttccaacttgcttac---attcctattgctgtgcttgcag---------------

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G28400.1 (Glycine max), 5'ss of exon 5
TTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccataactccatgccaatgttcttgctattttcttgtataaagccctatttgtccaatttgtttagttgtttactctcc-ttatgcttgcatgacatgacatgacag
| | |||||||| || || ||||| || |  || || |||||  || |||| ||||||||  | ||||||||||||| ||||| ||||||||| ||||||||   |  | |       | |||   ||       |   || ||  |    |      ||  |||  |      ||||||  ||   ||| ||    | |             
TCTGCATGATCCTTCTAAAGATACAGGTTTCGTTGGGTGTGCATTGTCAAGTAACATGGTACGCTTTTTCAAGACTGAAGATGAATCATGGAGTCATGAGgtacataaaaagtatatagtcaaaaatca-atccctaaattataggagaatcacaacatctcattaatcggaaggtttacattcagctattctatttttat------------

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 5'ss of exon 5
TTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccataactccatgccaatgttcttgctattttcttgtataaagccctatttgtccaatttgtttagttgtttactctccttatgcttgcatgacatgacatgacag------------------
  | |||||||| || || ||||| |||| ||| || |||||  | ||||||||||||||  |||||||||||||  ||||||| ||||||||||| ||||| ||   ||||    |||    ||||  | | |||   |||| | || || |   | |  ||||   |||||   |       | |     | ||  | ||   || ||                    
CCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgcggataa---tatg----tgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaag

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|29642050|gb|CB647057.1|CB647057
EST:     TGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: TGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|428075|gb|D24223.1|D24223
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|38468782|gb|CF952913.1|CF952913
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|218496469|gb|FG953873.1|FG953873
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|4968771|gb|AU065675.1|AU065675
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCA
EST: gi|29644289|gb|CB649296.1|CB649296
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATTTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|29638055|gb|CB643064.1|CB643064
EST:     CAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: CAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|58658655|gb|CK047335.1|CK047335
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|33799340|gb|CF325529.1|CF325529
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|218504274|gb|FG947023.1|FG947023
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCG
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCG
EST: gi|58654482|gb|CK043162.1|CK043162
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAC
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|29656380|gb|CB652655.1|CB652655
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATAAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|29667413|gb|CB663688.1|CB663688
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|58686485|gb|CK075172.1|CK075172
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|29642049|gb|CB647056.1|CB647056
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GGTGCTATATCTATAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAA
EST: gi|58594459|gb|CF992767.1|CF992767
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|38472891|gb|CF957023.1|CF957023
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|29641846|gb|CB646853.1|CB646853
EST:     CAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: CAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|66913768|gb|CX100616.1|CX100616
EST:     GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: GCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
EST: gi|29645926|gb|CB650933.1|CB650933
EST:     TTTTCAAGACTGCAGATGGATCATGGAGCCATGAG                         GTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA
genomic: TTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAA

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), 75 (downstream exon)
Score: 99

TTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccat ... gacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAAATGCCAGGACTGATAACTGATTTTGTTATCTCTCTGGATGATCGCTATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccataactccatgccaatgttcttgctattttcttgtataaagccctatttgtccaatttgtttagttgtttactctccttatgcttgcatgacatgacatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA