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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgatgaactagttgatcataaattctacattcgacgtagcgtctctactgtttttactgatctggccaccctgtttgttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGCAACAACGCCATCATCGCGCAGATGGCACGTAGCAGCCCACCGGAGAAGC

Basic information

species Oryza sativa
transcript LOC_Os01g70950.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70950.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G096037_T01 (Zea mays), 3'ss of exon 2
-----gtgagcgatgaactagttgatc--ataaattctacattcgacgtagcgtctctactgtttt-tactga-tctggccaccctgtttgttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGCAACAACGCCATCATCGCGCAGATGGCACGTAGCAGCCCACCGGAGAAGC
     ||        | |||      |   | | || ||     ||  |   ||  || |||| |  || ||| | ||| |||| | |||||||| | ||||||||||||| ||||| |||||||| || ||||||| |||||||||  ||||||| || | ||||||||| ||||||||  ||||||| |||| ||| |
gtgttgttccttcaaatctaaccacccttgtgagttgtatgcatgatttttggttcctgctgtatgatagtgactttgggcaccttatttgttgaaccagGTGATCCAAATCGACCCTAGGAACACAGAAGAAATGGAATTCTGGGACGGCAACAATGCAAACATCGCGCAAATGGCACGGGGCAGCCCTCCGGGGAAAC
















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|88963566|gb|CI029360.1|CI029360
EST:     TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACT                         GTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
genomic: TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACTgtgagcgatg ... gttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
EST: gi|88841248|gb|CI080702.1|CI080702
EST:     TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACT                         GTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
genomic: TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACTgtgagcgatg ... gttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
EST: gi|33793390|gb|CF322576.1|CF322576
EST:     TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACT                         GTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
genomic: TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACTgtgagcgatg ... gttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
EST: gi|218500544|gb|FG964041.1|FG964041
EST:     TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACT                         GTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
genomic: TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACTgtgagcgatg ... gttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
EST: gi|86494503|gb|CI137136.1|CI137136
EST:     TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACT                         GTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
genomic: TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACTgtgagcgatg ... gttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
EST: gi|25804324|gb|CA760285.1|CA760285
EST:     TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACT                         GTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
genomic: TCCGTGACATGGTTGCTGCCGCATTTTCGACATATGATCCAAATAGAACTgtgagcgatg ... gttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
EST: gi|88546073|gb|CI475681.1|CI475681
EST:     TCCAAATAGAACT                         GTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC
genomic: TCCAAATAGAACTgtgagcgatg ... gttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacgtagcgtctctactgtttttactgatctggccaccctgtttgttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGCAACAACGCCATCATCGCGCAGATGGCACGTAGCAGCCCACCGGAGAAGC
                 tgttttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgatgaactagttgatcataaattctacattcgacgtagcgtctctactgtttttactgatctggccaccctgtttgttgatctagGTGATCCAAATAGACCCCAGGAACACCGAGGAAATGGGATTCTGGGAGAGCAACAACGCCATCATCGCGCAGATGGCACGTAGCAGCCCACCGGAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC