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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccatccaaggtacatgcactatttagttcttttttaatttggtaatcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAGATACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATT

Basic information

species Oryza sativa
transcript LOC_Os07g08880.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 4
---cccatccaaggtacatgcactatttagttcttttttaatttggtaatcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCA-TTGACGAGAT--ACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATT-
     ||  ||        |    |   ||  |  | | ||      |||    |||  |   || ||      ||   | | | ||  ||| ||||||||||| ||||||||||||||| ||| ||||||||  |||   | |||| | || | || ||  |  |  || |||||||||||||| || |||    | | | |    
gcattcaaacatcaagtgaggggaaccaagcaccctctaaaaactacaatgtgaatt--gtagttatgcttc-taatagtataactttaactgatctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTT----TCACGTTTGAG
















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|88438337|gb|CI541081.1|CI541081
EST:     ATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: ATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|218495783|gb|FG965861.1|FG965861
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|88964512|gb|CI055208.1|CI055208
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|88831715|gb|CI369397.1|CI369397
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|88201730|gb|CI202085.1|CI202085
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|86544705|gb|CI184911.1|CI184911
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGTAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|88907070|gb|CI376142.1|CI376142
EST:     CTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: CTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|66921858|gb|CX108706.1|CX108706
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|88261442|gb|CI365018.1|CI365018
EST:     AGATGGCTGAGAATTCTCATTAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: AGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|89178434|gb|CI015139.1|CI015139
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCCAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|89178885|gb|CI391883.1|CI391883
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA-                         -AGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|88852528|gb|CI374296.1|CI374296
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|88838617|gb|CI376155.1|CI376155
EST:     CTGAGGATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: CTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
EST: gi|86531645|gb|CI171851.1|CI171851
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         CAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... atctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAGATACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATT
                                        gactaat  putative branch site (score: 2)
                                              tctcttc  CT-rich tract
                              atttcattt  TA-rich tract