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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatatcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC

Basic information

species Oryza sativa
transcript LOC_Os06g01390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 3
gtactaatatcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaatt-ttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
                         || ||     | ||    || | |   |  |     | ||  | |  |||||||  ||    |  | |  |||  || |     || |||   || |||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||| | |||||| |||| ||||| |||| ||||||||||||||| ||||||||||
-------------------------ca-tagaagattcataccacggaaggaacaccagatagttgctttgtacaagctttatcttctttttgttaact-tattacagacacaatacgatcttgcagGGCATGTTCGTTCCAGCTATAAAAGGCCAAGGAACTGAGGAGCAGCAGCACAAGTGGTTACCACTGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
gtactaatatcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
        | |    |||  ||     | ||  | |  || ||| ||   |    |     |  || ||| | |   ||    |  | | | |  |||| |        | ||| | || |||||||||||||||||||||||||||||||| ||||| ||||| ||||||||||| |||||| ||||  |||| |||| ||||||||||||||| ||||||||||
--------aacagatataagattcctgccattgaat--aacatatagtttttgtaca----agcttcatcaatattttc----accttacaagttacaaaa--------acaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 2
gtactaatatcgaccatattatcttcactatctactcca-atatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
    |||||| ||| |   | | |||||| || |    | ||||| |    |   |  ||     ||| |  || |  |   ||| ||               |||       || || |||||||||| |||||||| ||||||||  |||| ||||| ||||| || |||||| |||||||| | ||||| || || ||| | ||||||||||| |||||||| |
---ataatattgac-agggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtactaaatt--ttagttg--------------ttt-------atattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 3
gtactaatatcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
 || |||||| || |    | | |||||| ||   |  |||||| |    |   |  ||     ||| |  || |  |   ||| ||               |||       || || |||||||||| |||||||| ||||||||  |||| ||||| ||||| || |||||| |||||||| | ||||| || || ||| | ||||||||||| |||||||| |
ata-taatattgagcg-ggtgttttcactttccg-tggaatatatatattttgggtagcattgctttgtgtactaaatt--ttagttg--------------ttt-------atattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 3
gtactaat--atcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
|||| | |   || |   |  |     || | | | ||   ||||||           | |  |    |||  | | |   ||  || || |   ||   |    | |  || || || ||||||||||| |||||||||||| |||| ||||| ||||| ||||| || |||||| |||||||| | ||| ||||  | | | | ||||||||||| |||||||| |
gtacaattcagtcaattgtcctgatggcattcttttctttgatatac-----------tacctataaatatatatatggatga--aaatactgatgagataggtctagctcataaatt-attttgcagGGAATGTTTGTTCCTACTATCAAAGGACAAGGAACTGAGGAACAGCAGCAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGCTATGCCC

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
gtactaat--atcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
|||| | |   |  |   |  |     || | | | ||   |||||   | || ||       |  || ||  | |  ||| || |    |||||          | |  || || ||  |||||||||| ||||||||||||||||| ||||| ||||| ||||| || ||||||||||||||| | ||| ||||  | | | | ||||||||||| || ||||| |
gtacaattcagttaattgtcctgatggcattcttttctttgatatattac-ctaaaaagatatatattgatgaaaatactc-atga---gatagg--------tctagctcataaattc-ttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC

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|66919124|gb|CX105972.1|CX105972
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
EST: gi|58607678|gb|CK035711.1|CK035711
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
EST: gi|29630576|gb|CB635585.1|CB635585
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
EST: gi|58601479|gb|CK012007.1|CK012007
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
EST: gi|58682509|gb|CK071196.1|CK071196
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGGCCATGG-ACTGAAGAGCAGCAGAA
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGG-CCAAGGGACTGAAGAGCAGCAGAA
EST: gi|29666537|gb|CB662812.1|CB662812
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
EST: gi|58611759|gb|CK039471.1|CK039471
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGTAA
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAG-AA
EST: gi|88415359|gb|CI586565.1|CI586565
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGC
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGC
EST: gi|88411917|gb|CI571409.1|CI571409
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGG
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGG
EST: gi|29680079|gb|CB676354.1|CB676354
EST:     ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
genomic: ATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
EST: gi|2443069|gb|C74840.1|C74840
EST:     GATCTGCACTGG                         GGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG
genomic: GATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAG

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: 62 (upstream exon), 62 (downstream exon)
Score: 50

AAGAGGAGGCAAATTTGCTAAGGCTATACGTGGACCAGCCTGGTTATGTTGATCTGCACTGGgtactaatat ... tattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
            aattaat  putative branch site (score: 50)
                                          ttttatttt  putative PPT
                                   tgcaaaattttatttt  TA-rich tract