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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattgcccactcttgcaccaagttatacatgttcttggaagcaagacaaactgtatatcaccaagaattcaccttattttcgttttctctgcttcaag

Basic information

species Oryza sativa
transcript LOC_Os07g07000.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07000.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G044527_T01 (Zea mays), 5'ss of exon 11
ATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattgcccactcttgcaccaag----ttatacatgttcttggaagcaag-----acaaactgtatatcaccaag-------aattcaccttattttcgttttc-----tctgcttcaag
||||| ||||| ||||||||| | || || |||||||||||||||||||||||||| ||||||||||||||| ||  | | |  ||||   ||    || ||  |       ||| || |     | ||| |   ||  | | ||       |  ||||     | ||| ||||     |||  ||||||
ATATTTATGGACATGGCAGTTCTTGTCGAGGCTCAAGGAGACATGATCAACAACATCGAGACACATgtaagagttctctatttctgcattgagcctgttgtatgtaggacaagaaccatgtttcaataaattaattaatagcgagcttgatgagatcactcacatgtcgatttccatcctctttttcaag

upper sequence: LOC_Os07g07000.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G330772_T01 (Zea mays), 5'ss of exon 11
ATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattgcccactcttgcaccaagttatacatgttcttgg-aagcaagacaa---------actgtatatcaccaagaattcaccttattttcgttttctctgcttcaag
||||||||||| ||||||||| | ||||| || ||||||||||||||||||||||| ||||| |||||||| |||  | |||  ||||   |        |||    |  |||||                 | | ||  | ||||  || |    ||  ||   | ||||| ||||||
ATATTCATGGACATGGCAGTTCTTGTTGAGGCGCAAGGAGACATGATCAACAACATCGAGACCCATgtaagcattctctacttctgcattgaacctgttgtgtataggataagcatcgttttttttctttgttttgtaatagcaagc-ttgatggaatcatcccatcctctgtttcaag

upper sequence: LOC_Os07g07000.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G08080.3 (Arabidopsis thaliana), 5'ss of exon 13
ATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattgcccactcttgcaccaagttatacatgttcttggaagcaagacaaactgtatatcac--caagaattcaccttattttcgttttctctgcttcaag-----
|||||| ||||||||||||||||||||||||| |||||||| ||| |  |||| |||||  | || ||||       |   |  | ||  |   |    |   | |   || | |   |  ||  | ||||   ||       |    ||  |  |    | ||   |||      
ATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAGgtaatttggtactttttctacaatagagtcgttac-ctttcaaaaactaagtagtctaaagatcaaggcactgtaatagtacatactgatgggatttgtggcaaatatag

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|86415409|gb|CI069812.1|CI069812
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|25803804|gb|CA759765.1|CA759765
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|58593226|gb|CF991534.1|CF991534
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|86869572|gb|CI346432.1|CI346432
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|88266930|gb|CI368706.1|CI368706
EST:     TGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: TGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|88466365|gb|CI529774.1|CI529774
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|58596499|gb|CK007027.1|CK007027
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|88451245|gb|CI534238.1|CI534238
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|86832834|gb|CI332440.1|CI332440
EST:     CAGTTTTGNTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|88468042|gb|CI517501.1|CI517501
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|88964544|gb|CI069892.1|CI069892
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|86593575|gb|CI264454.1|CI264454
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
EST: gi|88297117|gb|CI545207.1|CI545207
EST:     CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT                         GTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC
genomic: CAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAAC

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), 70 (downstream exon)
Score: 5

ATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattg ... ctgcttcaagGTTTCAAATGCTACCAACCACATACAACAAGGCGTCAGTGCTCTACAGAACGCGAAGAAGCTCCAGAAGAACTCCAGGAAGTGGATGTGCTACGCCATCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACATgtaagaattgcccactcttgcaccaagttatacatgttcttggaagcaagacaaactgtatatcaccaagaattcaccttattttcgttttctctgcttcaag

- - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - -  AGGAGA