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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatcacaaaagagaggaaaatgaacatgcgttacgccttgctacgatgtaatttccatccttctacttctcttaagctaacaccatctgttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCTCCGGCTCCAGCAGTTGATCTGAGCTACGGTTCATACCCACCACCATATG

Basic information

species Oryza sativa
transcript LOC_Os03g42900.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42900.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G417223_T01 (Zea mays), 3'ss of exon 7
------caatcacaaaagagaggaaaatgaacatg-cgttacgccttgctacgatgtaatttcc-atccttctacttctcttaagctaacaccatctgtt--gcttgcagAATTTCATGGCAGAAGCT-CCTCAGGGCCCTC-----CTCCGCCAGCTTCTAACCCTCCGGCTCCAGCAGTTGATCTGAGCTACGGTTCATACCCACCACCATATG
          | |     |  | |  |||  | |  ||  |  |      ||| |  |  || | || || |   | || |||||||||      |  ||   ||||||||||||||||||||||||| || ||   ||  |     |  |||||||||| |||||||| || ||| |||||||||  ||||| || || ||||||||||      
gtaccttttccgccgtccattgcaccatggtcttaacgaaagacgaaagcacgtttcacctttcgatgctccccttgctgttaagctaattttgcccttttcacttgcagAATTTCATGGCAGAAGCTGCCCCACCACCACCAGGCCCGGCGCCAGCTTCCAACCCTCCCGCACCACCAGTTGATCCAAGCTATGGCTCTTACCCACCAC------
















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|66919597|gb|CX106445.1|CX106445
EST:     AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAG                         AATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
genomic: AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAGgtatattttc ... ttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
EST: gi|86845371|gb|CI340439.1|CI340439
EST:     AGATAATT-GTAGTGCATCCCAAGTCCAAACTGCCCAGCAAGTAGTCCAC                         AATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGGTTCTAACCCT
genomic: AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAGgtatattttc ... ttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
EST: gi|88265961|gb|CI376863.1|CI376863
EST:     GTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAG                         AATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
genomic: GTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAGgtatattttc ... ttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
EST: gi|88252304|gb|CI350732.1|CI350732
EST:     AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAAGTAGTCCAG                         AATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
genomic: AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAGgtatattttc ... ttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
EST: gi|3766837|gb|AU030947.1|AU030947
EST:     AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAG                         AATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
genomic: AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAGgtatattttc ... ttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
EST: gi|86887668|gb|CI311951.1|CI311951
EST:     AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAG                         AATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
genomic: AGATAATTGGTAGTGCATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAGgtatattttc ... ttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
EST: gi|88273252|gb|CI388708.1|CI388708
EST:     CATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAG                         AATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT
genomic: CATCCCAAGTCCAAACTGCCCAGCAACTAGTCCAGgtatattttc ... ttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtaatttccatccttctacttctcttaagctaacaccatctgttgcttgcagAATTTCATGGCAGAAGCTCCTCAGGGCCCTCCTCCGCCAGCTTCTAACCCTCCGGCTCCAGCAGTTGATCTGAGCTACGGTTCATACCCACCACCATATG
                              agctaac  putative branch site (score: 2)
     aattt  TA-rich tract