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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttaatatgctcattgctcttcctgtttattttgttgacttatgcatattagtaatttgttcatatttttatgctcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACCAGTGAAGTCAGTATATCATTGACACTAGATCCATCAAAACTATGGTGTC

Basic information

species Oryza sativa
transcript LOC_Os03g63330.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G024686_T01 (Zea mays), 3'ss of exon 9
gtattttaatatgctcattgctcttcctgtttattttgttgacttatgcatattagt-aatttgttcatatttttatgctcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACCAGTGAAGTCAGTATATCATTGACACTAGATCCATCAAAACTATGGTGTC
|| |||| || || || ||| ||| || ||| | |||| || | ||| ||||||||||||| | | |||||| |||||||||||||||||||| || ||||||||||| ||||||||||| ||||||||||| || || ||||| ||||||||||||||||||||| |||
gtgcattaagcaactgatg---tgtctcatttgtttgtttccactatacctatttgttagcttgatcatatttttatgtacattcgcagGTATTCTCAATATTTGAAGATTTGGGCATCTCTGTTGACTGTGTGGCTACTAGTGAAGTCAGCATCTCGTTGACTCTAGATCCATCAAAACTATGGAGTC

upper sequence: LOC_Os03g63330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S286_35V6.2 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------gtattttaat-atgctcat-tgctcttcctgtttatt--ttgttgacttatgcatattagta-atttgttcatatttttatgctcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACCAGTGAAGTCAGTATATCATTGACACTAGATCCATCAAAACTATGGTGTC
|| || ||| | ||| | | | | | || | | ||| || | ||||| ||||| |||| | |||| | ||||| ||| | | ||||||||| ||||| |||||||| ||| ||||| || ||||| |||||||||||||||||| | || ||| | || || ||| |
gtatggaagtgtaatctcatttagggatttggttgatatggttatgtgtttgcttcatgaaatacggtttacttgaattaagcttaagcgttttgtgcgattgatcgtctttggactagtaactttagtctgattgtttatatatcgtcattcttat-cagGTATTCACTACATTTGAAGAATTAGGGATCTCTGTAGATGTAGTGGCCACAAGTGAGGTCAGTATATCATTGACATTGGACCCAGCGAAGCTCTGGGAAC
















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|29614037|gb|CB619050.1|CB619050
EST:     TGGATATAGTGAGCACAAGGATGCTTGGCCAGTATGGTTTTCTGGCGAAG                         GTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACC
genomic: TGGATATAGTGAGCACAAGGATGCTTGGCCAGTATGGTTTTCTGGCGAAGgtattttaat ... tcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACC
EST: gi|29618752|gb|CB623764.1|CB623764
EST:     TGGATATAGTGAGCACAAGGATGCTTGGCCAGTATGGTTTTCTGGCGAAG                         GTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACC
genomic: TGGATATAGTGAGCACAAGGATGCTTGGCCAGTATGGTTTTCTGGCGAAGgtattttaat ... tcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACC
EST: gi|29683344|gb|CB679619.1|CB679619
EST:     TGGATATAGTGAGCACAAGGATGCTTGGCCAGTATGGTTTTCTGGCGAAG                         GTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACC
genomic: TGGATATAGTGAGCACAAGGATGCTTGGCCAGTATGGTTTTCTGGCGAAGgtattttaat ... tcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACC

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: 52 (upstream exon), 75 (downstream exon)
Score: 26

AGTATATTAACCAGCATTGTATTGAAGTCAAACATTACTATGCTGGATATAGTGAGCACAAGGATGCTTGGCCAGTATGGTTTTCTGGCGAAGgtattttaat ... tcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACCAGTGAAGTCAGTATATCATTGACACTAGATCCATCAAAACTATGGTGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttgacttatgcatattagtaatttgttcatatttttatgctcttgtgcagGTTTTCTCAATATTTGAAGATTTAGGTATCTCTGTTGATTGTGTGGCTACCAGTGAAGTCAGTATATCATTGACACTAGATCCATCAAAACTATGGTGTC
   tgttgac  putative branch site (score: 26)
 tgctctt  putative PPT
 atattagtaatttgtt  TA-rich tract