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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgtttttttttcccattatgcactactattgtatgaattgtctatactgtttgttactaataattaaatgtggtacctgccaatgtgcgttaaagctttga...

Basic information

species Oryza sativa
transcript LOC_Os03g21950.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G348729_T01 (Zea mays), 5'ss of exon 5
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgtttttttttcccattatgcactactattgtat-gaattgtctatactgtttgttactaataattaaatgtggtacctgccaatgtgcgttaaagctttga-
||| ||| ||||||| |  || ||| |||| ||||| ||||| |||||||||| |||||||||||| ||||||||||||||||||||||| ||||||||||||  | |    ||  || || || | ||   |  |||  || |||      || | |  |||   | | | ||   ||         ||     ||   | 
GGCAGCTGAGGAGGTCGTAGAGGGAAAGTTGGATGATCACTTCCCACTTGTTACCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgttggtgtcctacac-atccaatatttttacttcaaatcttccataaaaac-gtcaattttaaagtagtatagttgttgtttggaatggtagtccctgctaa

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G348729_T01 (Zea mays), 5'ss of exon 6
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgtttttttttcccattatgcactactattg-tatgaattgtctatac--tgtttgttactaataattaaatgtggtacctgccaatgtgcgttaaagctttga
||| ||| ||||||| || || ||| |||||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||  | |    ||| || || || | ||  |   |||  || |||    ||   ||   ||  | || |  || |   ||  ||||   ||    |||    
GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTAGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgttggtgtcctacat-atccaatatttttactccaaatcttccataaaacgtcaattttaaagtagtatagctgttgtttgg-aatggtagtccctgctaaa-

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 3
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgtttttttttcccattatgcactactattgtat-gaattgtctatactgtttgttactaataattaaatgtggtacctgccaatgtgcgtta-aagctttga
||| ||| ||||||| || || ||| |||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||   | |    ||  |  || || | ||   |  |||  || |||       | | |  |||   | | | |    |     | ||  |   || |  || 
GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTGGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcctacac-acccaatatttttacttcaaatcttccataaaaac-atcaattttaaagtagtatagctgttttttttttgaatggcaatccctgc

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 3
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttt-ttcccattatgcactactattgtatgaattgtctatactgtttgttactaataattaaatgtggtacctgccaatgtgcgttaaagctttga----
 || || || || || || || ||| |  || | ||||| ||||| || ||| | ||||||||||| |||||||| ||||| |||||||| || || ||||||  ||  || |   |    |||| |||| | |||  ||    ||   ||  |       |  ||||| || ||   || ||  |   |||| | | | |    
AGCGGCACAAGAAGTGGCCGAGGGAAAACTAAACGACCATTTTCCTCTCGTTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagttactgcttcctactattatttt-tgagctgcacctaaccttaatgttctgcatataaatatgttata-gctaacat---ttaaggatcttagatt

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G01930.2 (Glycine max), 5'ss of exon 3
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttt-ttcccattatgcactactattgtatgaattgtctatactgtttgttactaataattaaatgtgg-tacctgccaatgtgcgttaaagctttga
 || || || || || || || ||| |  || | ||||| ||||| || ||| | |||||||||||||||||||| ||||| |||||||| || || ||||||  ||  || |   |    |||| |||| | | |  ||    ||   ||       |     |  ||      |  |   |     | || |||  |   
AGCAGCACAAGAAGTAGCCGAGGGAAAACTAAACGACCATTTTCCTCTCGTTGTATGGCAAACTGGGAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagttactgcttcctactattatt-tgtcagctgcacctaaccttaaccttaaggttctgtatacaaacatgttatagctcacatttaaggatct-

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 4
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgtttttttttcccattatgcactactattgtatgaattgtctatactgtttgttactaataattaaatgtggtacc--tgccaatgtgcgttaaagctttga-
 || || || || ||  | || ||| |  || |||| || ||||| || || || ||||||||||| |||||||| ||||| |||||||| |||||||||||     |       | |    | || |  | ||  ||| |  | || || ||||     |  |  |  |  |  |  | || |||    ||   | | | | 
AGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCGTCATATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCCAATGAGgtaaggatcggtttatgtagcttcctgtcttctggtttgacgctgct-ttagttatatgcagatggaccttatttcgattccgatggaaattt--gttctaaa

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 5'ss of exon 1
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttt-----ttttttcccattatgcactactattgtat--gaattgtcta--tactgtttgttactaataattaaatgtggtacctgccaatgtgcgttaaagctttga
||| || || || || ||||| ||  ||||  ||||||| ||||| ||||| || ||||| || || ||||| || ||||| |||||||| ||||||||||||      ||| ||   | |     | |  ||| |    |||| ||  |  ||   | ||     | |  | || | |    | |   |   |   ||          
GGCAGCCCAAGAAGTGGCTGAGGGGAAGTTGAATGACCATTTTCCTCTTGTCATATGGCAGACAGGCAGTGGGACTCAAAGTAACATGAATGCCAATGAGgttagcacatttatttatacttcagtccataattatggtggaatggtacaggtagcatatggggtcattggtaaagtctctagctttttagcctcacttt---------

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S49_154V6.1 (Physcomitrella patens), 5'ss of exon 3
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttt------ttttcccatta-tgcactactattgtatgaa-----ttgtctatactgtttgttactaataattaaatgtggtacctgcc--aatgtgcgttaaagctttga-------------------------------------
 || ||    ||||| ||| | ||| || |   ||||||||||||||||||| | |||||||| || || ||||| |||   || ||||| ||||||||||| |||      || |||   |   |   |  || || || |      |||   ||| |  |  | |  |||  ||    | ||    |     ||  || ||       | |                                      
AGCGGCCAGTGAGGTAGCTCAGGGAAAGCTGACTGACCACTTTCCACTTGTTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctgaattgtcctgctggcgtcttgatactggataatgctctttgaacatattcctaatcatcaattcttgttcgaggacgttattcaaacatgagtcggcatgtagtctgcctcactcttttgaactttcgtgcgattttacag

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S9_243V6.1 (Physcomitrella patens), 5'ss of exon 3
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgtttttttttcccattatgcactactattgtatgaattgtctatactgtttgttactaataattaaatgtggtac-----ctgccaatgtgcgttaaagctttga-------------------------------------------------
 || |||   || || ||||||||| ||||    ||||| |||||||||||| | |||||||| || || ||||| |||| |||||||||| | ||||||||  ||    ||||   || ||| | |   |   |||  |   ||||||    ||||  || |    | |  | |       |  ||  |    ||||     |                                                  
AGCGGCTAGTGAAGTAGCTGAAGGAAAGTTGACCGACCATTTTCCACTTGTTGTTTGGCAAACGGGCAGCGGCACTCAAACCAACATGAACTCTAATGAGgtactt----cccaacttgtactgcgagcttgataatattgattactgtgctctactgttattcgcctatcattcagaagtcgagaacatcatctaaataacaggtggcgtacaattcatttagtcattttggctctttcatgtgcttgaatag

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|58692734|gb|CK081421.1|CK081421
EST:     TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAG                         GTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
genomic: TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
EST: gi|42592105|gb|CK738591.1|CK738591
EST:     GGGAGTGGCACACAAAGCAACATGAACGCCAATGAG                         GTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
genomic: GGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
EST: gi|33795747|gb|CF323743.1|CF323743
EST:     TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAG                         GTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
genomic: TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
EST: gi|33676561|gb|CF304800.1|CF304800
EST:     TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAG                         GTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
genomic: TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
EST: gi|33674910|gb|CF303149.1|CF303149
EST:     TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAG                         GTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
genomic: TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
EST: gi|568709|gb|D39558.1|D39558
EST:     TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAG                         GTTATTGCAAATAGGGCCGCTGAGATTCTTGGNCATAAGCGTGGCGAGAAG
genomic: TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
EST: gi|33676642|gb|CF304881.1|CF304881
EST:     TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAG                         GTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG
genomic: TTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 30 (upstream exon), 70 (downstream exon)
Score: 48

GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttttttt ... tgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgtttttttttcccattatgcactactattgtatgaattgtctatactgtttgttactaataattaaatgtggtacctgccaatgtgcgttaaagctttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA