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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgataacttgtatggtacctttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT

Basic information

species Oryza sativa
transcript LOC_Os03g13970.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147671_T01 (Zea mays), 3'ss of exon 4
----------gtatgataacttgtatggtacct-----ttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT
          ||  | |||||||||||  |  |     || | | ||| |   |||| ||||  || | |   | | |||| |||||||| |||||||||||| ||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||| | ||||||
gtaggcctgggtgggttaacttgtatgacaattattaattctctttgaatttaggttaatgaatctcgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 4
----------gtatgataacttgtatggtacct-----ttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT
          ||   ||||||| |||||          || | | ||| |    ||| ||||  || | |   | | |||| |||||||| |||||||||||||||||||| || || ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||| ||||||||
gtatgcagtggtggcataacttttatggcgatcattaattctgtttgaatttaagttaatgagtcttgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAGTTTTGGAGACCATTGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCCGATGAT
















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|163919850|gb|EG710352.1|EG710352
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|33657883|gb|CF280497.1|CF280497
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|33654150|gb|CF276764.1|CF276764
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATAC-ACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|58663975|gb|CK052661.1|CK052661
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAACAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|88358175|gb|CI605100.1|CI605100
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|33681541|gb|CF309780.1|CF309780
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|88434013|gb|CI586891.1|CI586891
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CC-TGTGAAATACGAGAAGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAA
EST: gi|33654616|gb|CF277230.1|CF277230
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|2309803|gb|C25958.1|C25958
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGNCAAGAAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAA
EST: gi|33681744|gb|CF309983.1|CF309983
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGANAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|88425160|gb|CI564677.1|CI564677
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCT
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCT
EST: gi|163926719|gb|EG713735.1|EG713735
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
EST: gi|218488524|gb|FG963297.1|FG963297
EST:     CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAG                         CCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA
genomic: CATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAA

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: 73 (upstream exon), 75 (downstream exon)
Score: 61

CTGAAGCAAATTTGGCTGCAGCAATTCAGGTTGCTCAGCTGGCTCTGAAGCATCGCCAGAATAAGAGGCAGCAACAGCGGATTATAGCTTTTATTGGAAGgtatgataac ... aatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatggtacctttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT
                                         gcctaat  putative branch site (score: 61)
                                               tctttc  CT-rich tract
           tttttatatga  TA-rich tract