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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcactattttttagataatggatagaaatccgatctctatatccacatgtaatatacccagctttcctcgctaatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g39570.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G407044_T03 (Zea mays), 3'ss of exon 1
cctcactattttttagataatggatagaaatccgatctctatatccacatgtaatatacccagctt--tcctcgctaatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG-
             |||||   |     | |||  |  |   ||   |  ||| | |   |    |   ||||| | | ||  | || ||  ||||   ||||||||||||||| || ||||| || ||||||||||||||    || || ||||||||||| || ||||||||  ||||  ||||  ||  |   | ||||  
------------gtagattgggtcctcacatc-aacttaactacttaagtgtgaaaaggcagattgggtcctcaccattg--tgttgcgcacatg---acagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCCAAGTACCTCCGCGGCTACTCTCTTCCACTGTAG-CCTTGCAGTCGTGATG

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------cctcactattttttagat-aatggatagaaa-tccgatctctatatccacatgtaatatacccagctttcctcgc-------taatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG-
                                                   |       |||  ||| |||| | ||  | |||  | | | |  ||  | ||  | |     |  |||    |       | |    | ||  |  ||  |  ||||||||||||||| || |||||||| |||||||| |||||    ||||| ||||||||||| || || |||||  |||| |||||  ||  |   ||||||  
gtatgtttcttatcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacac-atgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCCAAGTACCTCCGCGGTTACTCTCTTCCATTGTAG-CCTGGCATTTGTGATT

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G31810.3 (Arabidopsis thaliana), 3'ss of exon 10
--cctcactattttttagataatggatagaaatccgatct-ctatatccacatgtaatatacccagctttcctcgctaatgcatattccgtcca--tgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG
   ||     || | |  | ||     | ||    ||    | ||  | || |  |   ||  ||      |  | | | || ||||  |  ||    | ||||||| || ||||| || || |||||  |||  || ||||| || || || ||||||||||||||||| ||||||||||| ||   |  | |   | |   ||
cttcttctggttgtgtgtagaacaagaataagcttgacaagccatgactactttcagattatgca-----tcgtgttgacgcttattatgaacaatcaatcacagGTTGCAAGAACCGGTCGTGTGGCATTGGCTCGTGAATCGGGAGTGGACTCCAAGTACCTTCGTGGATACTCCTTTCCTTTAACAGGCTAAACCGTTGCAG

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|88488548|gb|CI425819.1|CI425819
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88539198|gb|CI468290.1|CI468290
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTTGTCCGCGAATCCGGTNTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|29676546|gb|CB672821.1|CB672821
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88538414|gb|CI467440.1|CI467440
EST:     ACAAGATGNTTGCATTACAAAGGCTNTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88477271|gb|CI414542.1|CI414542
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTNTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88512954|gb|CI440460.1|CI440460
EST:     CAANATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: CAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTAT-GGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88543743|gb|CI473778.1|CI473778
EST:     ACAAGATGGTTGCATTACAAAGGCTNTTGGACCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88284518|gb|CI405964.1|CI405964
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGGACAGGGCGAGTGGCGCTGGTCCNCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88832223|gb|CI017457.1|CI017457
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|15853702|gb|BI806498.1|BI806498
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88478672|gb|CI415943.1|CI415943
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88906495|gb|CI375567.1|CI375567
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGGGGTCGATTC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCC-GGTGTCGATTC
EST: gi|32948291|gb|BP184863.1|BP184863
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88508589|gb|CI436095.1|CI436095
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCNCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|86506103|gb|CI148736.1|CI148736
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88475065|gb|CI412336.1|CI412336
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         TTCGCCAGAACAGGGCGANTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|86522997|gb|CI163203.1|CI163203
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88481174|gb|CI418445.1|CI418445
EST:     ACAAGATGGTTGCATTACAAAGGGTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGTTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|33682201|gb|CF310440.1|CF310440
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88502715|gb|CI430221.1|CI430221
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         TTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88552259|gb|CI480930.1|CI480930
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88527127|gb|CI455250.1|CI455250
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         TTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTTTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|87021293|gb|CI295352.1|CI295352
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88273463|gb|CI393869.1|CI393869
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88513717|gb|CI441223.1|CI441223
EST:     ACAAGATGGTTNCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC

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: 66 (upstream exon), 75 (downstream exon)
Score: 38

CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatgtaatatacccagctttcctcgctaatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG
                         cgctaat  putative branch site (score: 38)
      taatata  TA-rich tract