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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga...

Basic information

species Oryza sativa
transcript LOC_Os01g04814.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggt-gcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga--
||| ||||||||||||||||| || || |||||||| |||||||| ||||| |||||||| |||||||| || || ||||||||||||||||||||||||||||  | |   | ||  | | || |   | | || |  | |  ||| |  | |    || ||||   | ||   |  |||   | | |  |  ||| ||   
CTTTATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGTAATGAAAGTGAAGCATCTAGGAGGATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaggtct---taatgctctcaaatgcacattattaacttgaatgcgagattatgttttaaaattgatcctaatatttgtagatgtcatcagtatactgtgt

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G088834_T01 (Zea mays), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttgg-acgtgttattcttagaatgataatga--
||||||||||||||||||||| || || |||||||| |||||||| ||||| |||||||| ||||||||||| || ||||||||||||||||||||||||||||| | |   | || ||   |||| |||       ||   |   || ||   ||  ||     |    | |  || ||  || ||  ||||    |  |  
CTTCATTGATGAAATTGATTCTTTATGCGGTCAACGTGGAGAAGGCAATGAAAGTGAAGCATCTAGGAGAATTAAGACTGAACTTCTTGTGCAAATGCAGgtgaagtat---taatgttgcaaactgttcccgtgtgggatgcacttagctagttatgttctgcttaggatggttacctgaaatgctgtgaatttagacaaag

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttggac-gtgttattcttagaatgataatga--------
 ||| |||||||||| |||||  | ||||||||||| |||||||| ||||||||||||||||| ||| | || |||||||| ||||| ||||| |||||||| |   | |  ||||  |   |  |  | |  ||  | ||  ||  |    |||||||||  ||   | ||| |  |   ||| || |  | |  ||  |        
ATTCGTTGATGAAATAGATTCTCTATGTGGTCAACGTGGAGAAGGGAATGAGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaa---taaatttatggtgcca--tggtgtagatacgctgattggaat---aatactttagttg-acatttgaattgcaatatcctgaacaagtcaagaagcttgagt

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G39410.1 (Glycine max), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaactttt-cttaatcaggtgcctgctacctgaatactttaaa-tgtgtacttggacgtgttattcttagaatgataatga
 || ||||| |||||||||||  |||||||||| || |||||||| || |||||||||||||| ||  | || ||||| || ||||| ||||| |||||||| |   ||    ||  || ||   ||    ||||   |     |    | |     |   ||  |||  | |   |  |||    |     ||||   |  
ATTTATTGACGAAATTGATTCCCTGTGTGGTCAGCGTGGAGAAGGCAACGAGAGTGAAGCTTCAAGACGGATTAAAACAGAGCTTCTGGTGCAGATGCAGgtaatagttttaatagtttgttggtttacatttaaattgcaatatatagcatatgcgcggcaagctgtcaaatcccagttgtatggccatatatgaatgt--

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G09300.1 (Glycine max), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttggac-gtgttattcttagaatgataatga--------
 ||| |||||||||| || ||  | |||||||| || |||||||| ||||||||||||||||| ||| | || |||||||| ||||| ||||| |||||||| |   | |  ||||  | | |   |    || | | ||      |      ||| ||||  ||   | ||| |  | ||||| || |  | |  ||  |        
ATTCGTTGATGAAATAGACTCTCTATGTGGTCAGCGTGGAGAAGGGAATGAGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaa---tgaatttatggtgtca---tggtgtagttacgt--taattggagtgatattttagttg-acatttgaattgcgttatcctgaacaagtcaagaagcttgagt

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G30910.1 (Glycine max), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaactttt-cttaatcaggtgcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga--
 || ||||| |||||||||||  |||||||||| || |||||||| ||||||||||||||||| ||  | || ||||| || ||||| ||||| |||||||| |   ||    ||  || |||  ||    || |   |     |    | |    || | || |   |     ||||  ||| ||  ||    |||      
ATTTATTGACGAAATTGATTCCCTGTGTGGTCAGCGTGGAGAAGGCAATGAGAGTGAAGCTTCAAGACGGATTAAAACAGAGCTTCTGGTGCAGATGCAGgtaatagttttaatagtttgttagtttacatttgaattgcaatatatagcatatgcacatcaagt---tgtcaagacgccttagtcccagttgtatagcccta

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga
 ||  ||||||| || ||||| |||||||||  ||| ||||||||||| |||||||||||||| ||  | |||||||| || ||||| ||||| ||||||||| ||   |||||||   |   |   | | |  ||   |   || || |||||   |     | || ||||     | ||  | ||||           
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcat---agcttatccgaactaaactccatg-tcttttagttg-tagctgaaatttccgtctctg-acttatctctttttcttttag-----------

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattt-tagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga-
 |||||||||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| ||  |  | || ||||| || |||||||| || ||||||||    || ||    |||  |  | | ||  |    |   ||  | | |     || ||| | |  |  | |   |    || |   || |   ||| | | 
TTTCATTGATGAAATTGATTCCTTATGTGGCCAACGAGGTGAAGGCAATGAGAGCGAAGCCTCCCGACGTATTAAAACAGAGCTTCTTGTTCAGATGCAGgtactcttataatggataagaacagccttaatcttccttctgtttacaagtattatgctt-agacct-cattgatataatttgtatgtaaatgcatactcat

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 5'ss of exon 3
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatact-ttaaatgtgtacttggacgtgttat-tcttagaatgataatga--
||||||||||||||| || || || ||||| || ||||||||   ||||||||||||||||||| |  | |||||||| ||||| |||||||| ||||||||    |||    | |  | |  |||  |   | ||     | |  |   |  ||| | || | | | |  ||  |  | || | ||||    |  |       
CTTCATTGATGAAATAGACTCCTTATGTGGCCAGCGAGGAGAGTCAAATGAGAGTGAAGCTTCTCGACGTATCAAAACAGAACTACTTGTGCAGATGCAGgta---tttgttgtgtggtgtggactggtgg-agtcttaaacttttttattatatattatttattattttattacatttattttatctttattttttgcctgca

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|300215967|gb|HO088593.1|HO088593
EST:     AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG
genomic: AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaatttta ... gaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG
EST: gi|33381146|gb|CF196489.1|CF196489
EST:     AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAG                         GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG
genomic: AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaatttta ... gaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA