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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctcttgtgcacgtatgtatcatctaatggttaccttttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g69920.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G423456_T01 (Zea mays), 5'ss of exon 8
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgt-gttttgcagtattgtttatactaatttggcatttctcttgtgcacgtatgtatcatctaatggttaccttttttcag---------------------------------------
| |||||||| || |||||||| |||||||||||    || ||||| || |||| ||||||||||||||||||||||||||||||||| ||||||||||||| ||| || |||     |  |  |  | |  |  || | |  | ||||  |   | | | ||  ||  |   |     | |    | || |||  ||| ||                                        
TAACTTGTGCTGATAGCGGGAAGAAAGCAATCACGCAACTGAAACCTCCTCACAGTTTTGATGCTTGTTTCATGGACATACAGATGCCTGAAATGGATGGgtgagttttatctttgtatattcatcatctcactatactttagacactatctgtacctatatccagttgataaacaatacttgctcttgtcaccgatttacattttcttgttctcttgtgtcatgcatttggtaccttgcag

upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G471529_T01 (Zea mays), 5'ss of exon 9
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctcttg--tgcacgtatgtatcatctaatggttaccttttt--tcag-------------------------------------------------
| |||||||| ||||| |||||  ||||||||||| |||| ||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||||| ||  |||        |   | ||  |     |  | |    |    || | ||||     |   |  |   |  |   |   | |  || |  || |  ||                                                   
TAACTTGTGCTGACAGTGGGAAGGAAGCAATCACACTGCTGAAACCTCCTCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCTGAAATGGATGGgtgagattttatcccttttatctttggatactcatcatctcaccatactttagacattatctgtaattatattcagttgatacacagtacttgctcttgtcatcgatttatatttgtcttgttctcttttgtcatgcatttggcacattttgcag

upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctcttgtgcacgtatgtat-catctaatggttaccttttttcag
|   |||||     || || ||| | || ||| | |   | || || || ||  | |||||||| ||||||||||| || || |||||||||||||||||||| || |   |    | | ||| | |||   | | |  |   |  | |||| | | |  | ||  | |  | |  |  |||  ||  |     ||  |||  
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactt-tctttcagaatctgataatttatcattttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc--

upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgca----gtattgtttata-ctaatttggcatttctcttgtgcacgtatgtatcatctaatggttaccttttttcag
|   |||||    ||| || ||| | || ||| | |   | || || || ||  | |||||||| ||||||||||| || || |||||||||||||||||||| || |   |    | | |||   ||  | |     |||| || ||| ||    |   ||||    | |  ||  |  ||  |   | |  |||  |        
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttttaatatctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc-------

upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 9
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctcttgtgcacgtatgtatcatctaatggt-taccttttttcag
|    || || || || |||| ||| |||||| ||||||| || || || ||| | ||||||||||| ||||||||||| ||||||||||||||||||||||| | ||           | ||| || |   ||| || || | |  | || |  || | |  |  | |  |    ||  | |  ||   |  |||| | |||
TGGTCTGCGCTGAGAGTGGGATAAAGGCAATCTCATTGCTTAAGCCACCTCACGAGTTTGATGCTTGCTTCATGGACATTCAGATGCCAGAAATGGATGGgtatgcct-----------gattg-gtatactagtttttttgaaa--agttcgaaatatgtaataagaaaattgaaatgtttttctgccctgtctttctgcag

upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv01s0010g03780.t01 (Vitis vinifera), 5'ss of exon 9
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttg---tgttttgca-gtattgtttatactaatttggcatttctcttgtgcacgtatgtatcatctaatggttaccttttttcag-----------------------
|    ||||||||||| |||||||  |||||| || |||| ||||| || ||| | |||||||| ||||||||||| || ||||||||||||||||| ||||| || | |    |   |  |||    | |||||    ||    | | ||| |    |   |||||  ||||  ||| ||| || |     | | ||| | |                          
TCGTCTGTGCAGACAGTGGGAAAAGTGCAATCCCACTGCTTAAACCTCCCCACGACTTTGATGCCTGTTTCATGGATATCCAGATGCCAGAAATGGACGGgtatgtatgtcgccatggtatttgatgcgatttgcttacatcaaattttcta-tcaaactcctctctactgcatctatctatgattttcgtttgagcttgtctttataaatgtgaatctcctcccacag

upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S252_49V6.1 (Physcomitrella patens), 5'ss of exon 13
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctcttgtgca-cgtatgtatcatctaatggttacctttt--ttcag--
||   ||||   ||||||| | |  |||||||     | ||||||| || ||||| |||||||| |||||||||||  | || |||||||||||||||||||| |  || |     ||| | | | ||       ||  || ||| | | | |     |||   | ||| | ||    | ||  | || ||  | |     ||||  
TTGAGTGTGTTCACAGCGGAAGAGCAGCAATCCAGAAGTTAAAACCTCCTCACAACTTTGATGCGTGTTTCATGGATGTGCAAATGCCAGAAATGGATGGgtatggtttcttccttactacatatattc------atgcttaatatttagt-gaaggctcttgagagcatcttactcctgatgcactgattttcatgaagctcagtc

upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 5'ss of exon 13
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctct-tgtgcacgtatgtatcatctaatggttaccttttttcag----
||   ||||   |||| || | |   || |||     | | || || || |||||||| ||||| ||||| |||||| | ||||||||||||||||||||||| |  |  |    ||||  | ||  |   |     |  ||  | ||  |    ||    ||   |  |   |  |   | |||| |    |   ||| | |    
TTGAGTGTGTTTACAGTGGAAGAGCTGCTATCCAGAAGTTGAAGCCTCCCCACAATTTCGATGCCTGTTTTATGGACGTGCAGATGCCAGAAATGGATGGgtagggttccttc--cactcttagtcatccac-----tcgttgcaatagctgcatataagcctgcattaaaacaaatggtaactaaagagctcaagtttgctgaaat

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|58688918|gb|CK077605.1|CK077605
EST:     CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGG                         GTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
genomic: CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttt ... cttttttcagGTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
EST: gi|428793|gb|D24949.1|D24949
EST:     ACAGATGCCAGAAATGGATGG                         GTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
genomic: ACAGATGCCAGAAATGGATGGgtaagtcttt ... cttttttcagGTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
EST: gi|58588803|gb|CF987111.1|CF987111
EST:     CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGG                         GTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
genomic: CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttt ... cttttttcagGTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
EST: gi|58594894|gb|CF993202.1|CF993202
EST:     CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGG                         GTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
genomic: CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttt ... cttttttcagGTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
EST: gi|27334353|gb|CA882804.1|CA882804
EST:     CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGG                         GTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
genomic: CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttt ... cttttttcagGTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
EST: gi|38565686|gb|CK085139.1|CK085139
EST:     CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGG                         GTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG
genomic: CACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttt ... cttttttcagGTTTGAAGCCACTAGAAGGATTAGAGTGATGGAAAGAGATCTAAATGAGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctcttgtgcacgtatgtatcatctaatggttaccttttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG