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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatttttattatagttgcattgtatccacattacatggagttgttattataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG

Basic information

species Oryza sativa
transcript LOC_Os09g13870.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024615_T02 (Zea mays), 3'ss of exon 3
ttttatttttattatagttgcattgtatccacattacatggagt--tgttattataactctagttactcactttgct--ttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGAT-GTTACACTATAAAGTCCCATGGAACCAAAGTGGCGA--GACTTCACATGTACGACT--GGATAATACTTCTACTCCTTG
           |||  ||   |    |   | ||  |||||| |  | ||   |  | |  |  |       | | |  | ||| |  |  ||| | |   |  |||    ||    || |  | | |   || |||  |   ||    |||||   |  ||  ||  ||||| | || | | |    ||  |||||     |   |||
----------gttagggtcttac-acaattagatcccatggaatgatattggcaagattacacatgtatgactggataatacttctcctccttgctgtc--atagACGGGCTGTTGAATATAATTGAACCATTTCACCGTTTTGT----TGGAAAAGACATGATGACCGACTTGAGATATCCTATGAAGGGCAATACAGTGCCATTTTG

upper sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G050658_T02 (Zea mays), 3'ss of exon 2
---ttttatttttattatagttgcattgtatccacattacatggagttgttattataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
   |   |||  | ||  ||| ||  || | ||       |  || |||    | | | | ||  | ||   ||| || ||||  | | |||||| |||| |||| |||||||||||    ||||| | ||||||||| |  ||||||||||  | | |||| ||  | |||||||| ||||||||||||||||| |||||||
tagtaacattgatcttgcagt-gctgtgaagcccttgagaactgaattgcagctgttattgtaact-ctggattttctctcttactctctttgtt-tttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATGATATTGGCAAGGTTGCACATGTATGACTGGATAATACTTCTCCTCCTTG

upper sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024615_T01 (Zea mays), 3'ss of exon 2
-ttttatttttattatagttgcattgtatccacattacatggag--ttgttat-tataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
 |  || |   |    ||    ||||| | |||  |  | | |   || | || |  |||| || | |||   |||    ||| || |   ||||| |||| |||| |||||||||||    ||||| | |||||| || |  ||||||||||  | | |||| ||| | |||||||| ||||||||||||||||| |||||||
atactaatggaacctgagaactattgt-tgcaccctgtacgaaagattatcatgtgcaactttactcactggtttt-tgctctcgt-actcttgtt-tttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATGATATTGGCAAGATTACACATGTATGACTGGATAATACTTCTCCTCCTTG

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|88363440|gb|CI618001.1|CI618001
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29640276|gb|CB645285.1|CB645285
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|88732308|gb|CI755485.1|CI755485
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|13896471|gb|AU182807.1|AU182807
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|88355849|gb|CI626290.1|CI626290
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29671233|gb|CB667508.1|CB667508
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29642638|gb|CB647645.1|CB647645
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|88350748|gb|CI619006.1|CI619006
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29642303|gb|CB647310.1|CB647310
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|300215590|gb|HO088216.1|HO088216
EST:     CGAGGAGCCGCTCGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: CGAGGAGCCGCT-GGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|88454303|gb|CI569875.1|CI569875
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|88407270|gb|CI583728.1|CI583728
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
                 tactcac  putative branch site (score: 1)
                                    ttatgtttgttattt  TA-rich tract