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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcagtgctatcctttgcttaatttgtccgcttcaacttgttttagtctaaattgtctaattttcattggtattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAAACTTGCATTGCAACCATGCTTGATCCTGGTGCAAAAGAGTTTAGG

Basic information

species Oryza sativa
transcript LOC_Os11g29370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 2
-gttatcagtgctatcctttgcttaatttgtccg---cttcaacttgttttagtctaaattgtctaattttcattggtattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAAACTTGCATTGCAACCATGCTTGATCCTGGTGCAAAAGAGTTTAGG
  || | | ||||  |   |  ||||||| || |   ||||  ||||||||  ||| ||   |||| ||| | ||||| ||||| |||| |||||||||||||||||||||||||| ||||| |||||||| || || |||||||| ||||| |||||    ||||||||||| ||||| || 
gtttgtgaatgctccctcctttttaatttttctgttgcttctgcttgttttgatctgaaaactctagtttcctttggtgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA
















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|29671699|gb|CB667974.1|CB667974
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|218485973|gb|FG956977.1|FG956977
EST:     CTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: CTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|29634818|gb|CB639827.1|CB639827
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|58696100|gb|CK084787.1|CK084787
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|29634836|gb|CB639845.1|CB639845
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|29631427|gb|CB636436.1|CB636436
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|14191667|gb|AU183878.1|AU183878
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|29674778|gb|CB671053.1|CB671053
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
EST: gi|29686092|gb|CB682367.1|CB682367
EST:     GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAG                         GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA
genomic: GGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAA

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: 74 (upstream exon), 74 (downstream exon)
Score: 181

TGTGCTGTCAGCAGATGGGAAGGTGCTCTCCTCACCTGTATCAAAGCCATGGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgttatcagtg ... tattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAAACTTGCATTGCAACCATGCTTGATCCTGGTGCAAAAGAGTTTAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccgcttcaacttgttttagtctaaattgtctaattttcattggtattttgcagGCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAAACTTGCATTGCAACCATGCTTGATCCTGGTGCAAAAGAGTTTAGG
                             gtctaat  putative branch site (score: 181)
                       taaattgtctaatttt  TA-rich tract