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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatgatatgttgggattactgaattatcattaatgatttgtttagctatcagtagtgcgatggtaatacatcaaggccagggtctcccgggttc...

Basic information

species Oryza sativa
transcript LOC_Os07g08880.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 4
TGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatgatatgttgggattactgaattatcattaatgatttgtttagctatcagtagtgcgatggtaatacatcaaggccagggtctcc----cgggttc-
 ||||| ||||| ||||||||||||||||||| |||||| || |||||||| ||||||| ||||||||| |||||||||||||||||||| |||||||||||||   |  | ||| ||  | |      ||||||||  ||  |    | ||||||  ||  | | || |        | || |     |  |    |||||   
AGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccac-acatgatgttagtttctgcttatcattggtg--taagcttgctatc--taagggggtgattggttccaagggactaaaccgtcatatcgggtgtc
















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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatgatatgttgggattactgaattatcattaatgatttgtttagctatcagtagtgcgatggtaatacatcaaggccagggtctcccgggttc

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA