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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctcagctttccccaattgtattagagaaaatggcatccaatttaatcctgtgataaactctttaatgaatcaaccgagacaaagtaacttgcttcctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG

Basic information

species Oryza sativa
transcript LOC_Os04g56980.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56980.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G035325_T01 (Zea mays), 3'ss of exon 2
gtaatctcagctttccccaattgtattaga---gaaaatggcatccaatttaatcctgtgataaactctttaatgaatcaaccgagacaaagtaacttgcttcctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG
         |   | | |||||   ||| |   |||| || ||  |  | || ||   || |  ||||||| |   ||  ||      ||| |||  |     || |||||||||||| |||||||| |||  ||||||  ||||||| |||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||
---------gtactactcaatttctttacaatagaaattgacacactctatactctactggt--actctttgaatgattgactctaggaaattaatgt-tagtcttcattcagATTGTGAAGCAGCTATGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATCATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: LOC_Os04g56980.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G124502_T01 (Zea mays), 3'ss of exon 2
gtaatctcagctttccccaattgtattagagaaaatggcatccaatttaatcctgtgataaactct---ttaatgaatcaaccgagac---aaagtaacttgcttcctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG
    |   |  ||||    |||||  ||||  || |  ||  |  | || || | || ||  || |   | | ||| || |  ||| |   ||| ||| |      ||  ||||||||||| |||||||| |||  ||||||  ||||||| |||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||
---gtactaaatttc----attgtgataga--aatttacacactctgtactcttctggtactctttgaatgattgactctatagagtctagaaaataaatattagtctttattcagATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATTATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: LOC_Os04g56980.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 2
gtaatctcagctttccccaattgtattagagaaaatggcatcc--aatttaatcctgtgataaactctttaatgaatcaaccgagaca--aagtaacttgcttcctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG
         | ||   || ||  | ||  ||    | |  | |  |||  |    | ||||| | | |  |  ||     |  | |     |||||||    |      || ||||||| ||||| || |||   || ||  || |||| ||||| ||||||||     |||||||||| ||||| |||||||||||||| |||||||| ||||
---------gtttgtaccgatatttttgaagcttgttgtttgcttaatgcataattttgatatagtttccagcgagatttctaaaatgtggagtaactgtggt------tttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG

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|58601754|gb|CK012282.1|CK012282
EST:     CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAG                         ATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAGTAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAGgtaatctcag ... ctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
EST: gi|58681042|gb|CK069729.1|CK069729
EST:     ACCGTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAG                         ATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAA
genomic: ACC-TGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAGgtaatctcag ... ctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAA
EST: gi|84117678|gb|CD151445.1|CD151445
EST:     CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAG                         ATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAGgtaatctcag ... ctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
EST: gi|27576903|gb|CA999597.1|CA999597
EST:     CAAGAACTCAG                         ATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
genomic: CAAGAACTCAGgtaatctcag ... ctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
EST: gi|88693532|gb|CI737107.1|CI737107
EST:     CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAG                         ATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAGgtaatctcag ... ctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
EST: gi|29660434|gb|CB656709.1|CB656709
EST:     CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAG                         ATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAGgtaatctcag ... ctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCT

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: 48 (upstream exon), 62 (downstream exon)
Score: 13

AAAGCGGAAACGAGGTGGGCCTGGTGGTTTAAATAAAGTTTGTGCAATCTCACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAGgtaatctcag ... ctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataaactctttaatgaatcaaccgagacaaagtaacttgcttcctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG
                               aagtaac  putative branch site (score: 13)
                                     cttgcttcctccattc  CT-rich tract
          tttaatgaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctcagctttccccaattgtattagagaaaatggcatccaatttaatcctgtgataaactctttaatgaatcaaccgagacaaagtaacttgcttcctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA