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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataactctcttcttggaaactaaatatcatatttgaaactattaagagttaccttgtttgtaacactgaacattcttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC

Basic information

species Oryza sativa
transcript LOC_Os08g23440.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G449569_T01 (Zea mays), 3'ss of exon 1
gtataactctcttcttggaaactaaatatcatatttgaaactattaagagttaccttgtttgtaacactgaacattcttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC
                    ||| | ||||   ||||  | ||   |    |||  | ||||||||  |     | |||    ||||||||||||| |||||||||||||||||||||||||||||| ||||||||||||| |||||||||||||| |||||||| |||||||||||||| |||||
---------------gtacgactgactatctgctttgcgaatacataatcgtacaat-tttgtaacctttgg--tcctttctgcagCAAACCAAGTCCATCCTAAGAATTGGTACCCCATTCCTCTGGTATTCTGCCGTCCATGGGGTAAACTTCCGGAAAATGTTCCTTGTCATCCAAAACTTGC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G113276_T01 (Zea mays), 3'ss of exon 7
gtataactctcttcttggaaactaaatatcatatttgaaactattaagagttaccttg----tttgtaacactgaacattcttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC
                 |   || | ||||   |||| || || | |    ||| |      ||||||||  ||    | |||    ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| || |||||||| |||||||||||||| |||||
---------------gtgcggctgactatctgctttgcaattacttaatcatacttaacaattttgtaactttgg---tcctttctgcagCAAACCAAGTCCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCATGGGGCAAACTGCCGGAAAATGTTCCTTGTCATCCAAAACTTGC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 11
---gtataactctcttcttggaa----actaaatatcata--tttgaaactatta-agagttaccttgtttgtaacactgaa---cattc-ttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC
   ||| ||    |||  | | |     |     ||  ||  ||    | ||||  | | |||  ||| |  |   ||| |    | ||| || |   ||||| ||||||||| || ||||||||||| || ||||| ||| |||| ||||| || ||||| ||||| ||||||||||| || |||||||| || |||||
cacgtagaaggagctttatagcattatgccgcccattttagtttctccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
---------gtataactctcttcttggaaactaaat--atcatatttgaaactatta-agagttaccttgtttgtaacactgaac--attcttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC
          | || || | | | | |    |   |  || |||| || |  | ||| |     | | ||||  ||  | | | |  ||| |     |||||| ||||||||| || ||||| ||||| || ||||| || ||||||||||| || ||||| || || ||||| ||||| || || || || ||  | ||
tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcatgttttatatgaacatcatgttcttattatttacctcattatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC

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|58671906|gb|CK060592.1|CK060592
EST:     TAAGAGTGCATACTTTCAATTGGCACTACGAAGTCTCAGATCATTAGGAG                         CAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATT
genomic: TAAGAGTGCATACTTTCAATTGGCACTACGAAGTCTCAGATCATTAGGAGgtataactct ... cttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATT
EST: gi|29686364|gb|CB682639.1|CB682639
EST:     TAAGAGTGCATACTTTCAATTGGCACTACGAAGTCTCAGATCATTAGGAG                         CAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCC
genomic: TAAGAGTGCATACTTTCAATTGGCACTACGAAGTCTCAGATCATTAGGAGgtataactct ... cttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCC
EST: gi|58671465|gb|CK060151.1|CK060151
EST:     TAAGAGTGCATACTTTCAATTGGCACTACGAAGTCTCAGATCATTAGGAG                         CAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCC
genomic: TAAGAGTGCATACTTTCAATTGGCACTACGAAGTCTCAGATCATTAGGAGgtataactct ... cttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCC

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), 64 (downstream exon)
Score: 13

TATTACTATGTGAGCTTAAAAGGTAAGGCTGGAGACTGGGGAGATGGATTTAAGAGTGCATACTTTCAATTGGCACTACGAAGTCTCAGATCATTAGGAGgtataactct ... cttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgaaactattaagagttaccttgtttgtaacactgaacattcttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC
                            ttgtaac  putative branch site (score: 13)
                                           ttcttgtc  putative PPT
      aaactattaa  TA-rich tract