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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

Basic information

species Oryza sativa
transcript LOC_Os01g16900.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 2
-----aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
        || |  | ||||  |   | ||||   | |    ||| |     | |    ||| | ||| || ||||| | |     |||  |||||   |||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||||| |||
gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgtttctatgatgtcttaatat-----ttttgttttgtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG

upper sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 2
----aaatggtgccaagtgccttctgat-catgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
    || | |||      |     |||| |||| | || ||  | ||||||||||  ||      | |  |  |||| | |    ||||   | |||  |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||
tgttaattagtggatgaagttcattgatgcatgatatccgagaaggtagctcgtttctaca---atgtcttgacttaatat--tttttttgctctgcgctttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG

upper sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 1
aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
   | ||  |  ||    |    |  |   |||  |  |  |  || | |    || ||| | | ||      | | |  | || || |||   |  | || ||||| | |  || |  || ||||||||||||||||| |||||||| || || ||| |||| || |||||  |||| |||||||| |||||||| || |
-ttttgtttcttgttatgtagatttgtatattcatagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactgttgtaatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG

upper sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 1
aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
   | ||  || ||    |    |  |   |||  |  |  |  |  | |    || ||| | | ||     ||   || | || ||  || | |  | || ||||| | |  || |  || ||||||||||||||||| |||||||| || || ||| |||| || |||||  | ||||||||||| |||||||| ||||
-gtttgttgcatgttatgtagatttgtatgttcatagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgctgttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG

upper sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------aaatggtgccaagtgccttctgatcatgctttctgactatgta-gctcgttcttatgtatttattatatcttagtttgaacttttcctttt---gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
                                               ||   |  | |    | ||  |    |   | | |||| | |  ||  |  | |||    | || ||  |   |  |||| | |||    ||| | ||||| || |     || || |||||||| || |||||||||||||||||||| || ||  | ||||| |||||| |||||||  |||| ||||||||  | |
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggca-attttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG

upper sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ18109 (Selaginella moellendorffii), 3'ss of exon 2
aaatggtgccaagtgccttctgatcatgctttctgact------atgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
   | |||        | | ||       |||    ||        | | | |  |  || |     | | | ||| | || ||   |||| |  ||    |  || | ||||| | ||| || || || |||||||||||||||||||||||||| |||  | | |||||||  || |  || ||| | || |  || ||| |||
--tttgtgtttgccctcctttggctgcttttttcttctcaattcgcgcaacacagtgctaagagaacagtctttctcacttcgatagtttcttcatg----tgtagATTTTCAAGGCTGCGGGCGTTCCCATAGAATGGGAAGAACACTATGTTGGGACAACACTGGATCCCAAGACGGGAAGCTTTGTCACGTACGACAGCATGG

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|33793926|gb|CF322851.1|CF322851
EST:     TCTTTCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCATTCTT                         GTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
genomic: TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAGgtacggaatt ... gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
EST: gi|29639681|gb|CB644690.1|CB644690
EST:     TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
genomic: TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAGgtacggaatt ... gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
EST: gi|29664534|gb|CB660809.1|CB660809
EST:     TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
genomic: TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAGgtacggaatt ... gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
EST: gi|29619530|gb|CB624542.1|CB624542
EST:     TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
genomic: TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAGgtacggaatt ... gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
EST: gi|58656605|gb|CK045285.1|CK045285
EST:     TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
genomic: TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAGgtacggaatt ... gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
EST: gi|58654655|gb|CK043335.1|CK043335
EST:     TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCACTAGAATGGGAAGAACACTATGTTGGT
genomic: TCTTCCCAGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTCAAGCAGgtacggaatt ... gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
                                  cttttccttttgctgt  CT-rich tract
      ttatgtatttattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT