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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

Basic information

species Oryza sativa
transcript LOC_Os01g36950.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
-------------------------atattt-ctagcaactctgataatttttactactcgctaattacgagtttattatt-ttgtgaattattgcctaattacat--------acttatttc---tttttcattc---agGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                          ||    ||||| | |  | |  ||     | || |||  ||    |||   | |  |||    || ||   |   |  ||        ||    |||   |  | |  ||   |||| |||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| |||
gtacagtacagcacagcacagcacagtagccactagccagttcg-tggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AC207342.3_FGT008 (Zea mays), 3'ss of exon 2
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgc--ctaattacatacttatttctttttcatt--cagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
          |    | |   |||       |  || |||| |   |||    |||  |       |||  |||    |  |   ||    ||   ||   ||||| || ||||| ||||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
-------gtacggtacagtacattacagtagccagccaattcctgatttgccttttcatcttcatctgcatctatgctctcatggatccggttccgatcaccagGCCGCCAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------atatttctagcaactctg--ataattt---ttactactcgctaattacgagtttattattttgtgaattattgcc-taattaca-tacttatttcttt------ttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                                                                              ||| | |  |    |  ||   ||     |  |||     |||  |    |||  | |  | ||   |  |  |||||| | || ||| |  ||       ||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||| ||||||||||| || || || || |||||||| |||
gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattaggccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------atatttctagcaac---tctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG----------------
                                                                             |  || ||| |    |  |   || | |  |||    ||    | |   | | |||    | | || |   | |||| ||  ||  |    |||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||||||||||||||| || || || || |||||||| |||                
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacct-ttagcagctatggtctaattaaaggcaataataa-tgattaaatgtttggtggggttt-gttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------atatttctagcaac---tctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                                                                             |  || ||| |    |  |   || | |  |||    ||    | |   | | |||    | | || |   | |||| ||  ||  |    |||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||||||||||||||| || || || || |||||||| |||
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacct-ttagcagctatggtctaattaaaggcaataataa-tgattaaatgtttggtggggttt-gttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------atatttctagcaa-ctctgataatttttac-----tactcgct--aattacgagtttattattttgtgaattattgcctaattacatacttattt-ctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                                    || |||  | |  || |     ||||  |     || | | |  |||    ||    | || || || ||||| ||   ||||| || |  | | ||| |   |||||||||| |||||||| ||||||||||| ||||| || || |||||||||||||||||||| ||||| || ||||||||||| |||
gtttgtatttctttctaagaatcataaactctgcagtaattcatgtattcttttggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattat-gcaccattacctaatgttatacttgtatgttcagGCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                      |   || ||| |  ||| | |   |||    || |     |  |||      || | | |  | ||  |   || |||||  | || ||||| ||  | ||||||||| | || |||||||||||||||||||||| ||| |||||| | ||||| || |||
---------------------gtacgtattacac-ttaagtgcttctttgccgttgtcc---tctttgaaactctaaagaatc-tatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 2
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                   |||   | ||  ||| |  |    |  ||| | |   |     ||  || | | |  || |||| || | |     | ||||||||||| ||||| ||  ||||||| ||||| || |||||||| ||||||||||| |  || || || || ||||||||||||
------------------gtaaagct-acctctctcgca----ggatttgtgacact-catgttgatggcgagtc-caaactt-ttgcgtgactctacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ18285 (Selaginella moellendorffii), 3'ss of exon 2
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                   |||   | ||  ||| || |    |  ||| | | | |     ||  || | |||  || |||| || | |     | ||||||||||| ||||| ||  ||||||| ||||| || |||||||| ||||||||||| |  || || || || ||||||||||||
------------------gtaaagct-acctctctctca----ggatttgtgactct-catgttgatggcgaatc-caaactt-ttgcgtgactctacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG

upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                      |   || ||| |  ||| | |   |||    || |     |  |||      || | | |  | ||  |   || |||||  | || ||||| ||  | ||||||||| | || |||||||||||||||||||||| ||| |||||| | ||||| || |||
---------------------gtacgtattacac-ttaagttcttctttgccgttgtcc---tctttggaactctaaagaatc-tatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

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|570114|gb|D40963.1|D40963
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGTTTTGGCGGAACAAACATCGATCCGACGGCGTTGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|9884513|gb|BE607346.1|BE607346
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG
                      gcctaat  putative branch site (score: 3)
                                   cttatttctttttcat  putative PPT
                         taattacatacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT