Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaagatcatttgacaatctaaactacccatatgcttaggttccttgatggttctgtatgatttccccatgaaacatctttattaacttcagttctataaactattgttgtctttcctcaaaattacag

Basic information

species Oryza sativa
transcript LOC_Os04g40840.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 3
TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaag-atcatttgacaatctaaactacccatatgcttaggttccttgatggttctgtatgatttccccatgaaacatctttattaacttcagttctataaactattgttgtctttcctcaaaattacag
|||||||||| || ||||| |||||||| || |||||||| |||||| |||||||||| |||||| |||| |||||||||||||| ||||| ||||| ||||||| |||||   | ||| |  |     | | |  |||  |   || |       | |||  || ||  |   || ||  ||| || || |   | || || |   ||| | ||  |||  ||||  ||
TTCATGATGCTTTGTCGGGGCACACTTCAGCAAATGTTGAGGAGGCTATTTGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatcatcgcataat-tggatggtgcttcttattacttcaattcaaaag---gaatgtgttgcctttcccacttccctatgaatttaatcccaatgaaat---gtttttttctctcggaattctag

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G359735_T03 (Zea mays), 5'ss of exon 3
TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaag-atcatttgacaatctaa-actacccatatgcttaggttccttgatggttctgtatgatttccccatgaaacatctttattaacttcagttcta-taaactattgttgtctttcctcaaaattacag
|||||||||| |||||||| ||||||||||| |||||||| |||||| |||||||||| |||||| |||| |||||||||||||| ||||| ||||||||||||| |||||   | |||   |   | |  ||   |||    | |   | |    ||| ||  ||  || |          ||   |||||| | | | | || | || || | ||  ||   ||||  ||
TTCATGATGCTTTATCGGGTCACACTTCTGCAAATGTTGAGGAGGCTATTTGTTATTCGGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAGACgtaagtatcatcgcagaattggatgttgcttat-cacttttcattcaaaaggaaagtgt-tgtcttttccgt--------cctagggacttcaatcccagtgaaatgtt-tttttttatcttggaattctag

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 3
TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaagat--catttgacaatctaaactacccatatgcttaggttccttga---tggttctgtatgatttcccca-tgaaacatctttattaacttcagttctataaactattgttgtctttcctcaaaattacag
|||||||||| || || |||||||| ||||| ||||| |||||||| ||   ||| || || ||||| |||  ||| |||||||||||||||||||| ||||||| |    |||    || || | |  | ||||   |       | ||   | | ||||   |   |   || | |    ||||| |    ||  |||                                   
TTCATGATGCTTTGTCTGGACACACATCTGCCAATGTGGAAGAGGCAGTGGCTTACTCTGAGCATGGGGCAACCAAGTGTATTGGCATGACAATTGAAACgtaagttgctgtttaggtatatacatttgcaatatttgtgaaagtttggagccttggtctgctggtcatgtacagttatgtgtctttttcttttttggtt-----------------------------------

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 3
TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaagatcatttgacaatctaaactacccatatgcttaggttccttgatggttctgtatgatttccccatgaaacatctttattaacttcagttctataaactattgttgtctttcctcaaaattacag
|||||||||| || || |||||||| ||||||||||| |||||||||||    || || || ||||| |||  ||| |||||||| ||||| ||||| ||||||| |   || | | |    |        |  ||| |      || ||||   |||   || |           ||||| ||   || |     ||||   || ||                     
TTCATGATGCTTTGTCTGGACACACATCTGCTAATGTGGAAGAGGCTGTGGCATACTCTGAGCATGGGGCAACCAAGTGTATTGGTATGACGATTGAAACgtaagttg--ttaatatttgtgaaagtttggagccttgg----tctgctggtcaagtacagttacgtgtctg--tttctttttttggttaataaaaataatgcatggt---------------------

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 3
TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaagatc-atttgacaatc-taaactacccatatgcttaggttccttgatggtt--ctgtatgatttccccatgaaacatctttattaacttcagttctataaactattgttgtctttcctcaaaattacag
|||||||||| ||||| |||||||||||||| || ||||||||||| |||  ||| || |||||| |||||   ||||| ||||| ||||||||||| |||| || || ||     |||| |  || ||   ||   ||    ||  |  |  ||  ||  ||| |||| | |  || | |   || || ||  |  |  |                                
TTCATGATGCTTTATCAGGACACACTTCTGCCAACGTTGAAGAGGCAGTTGCTTACTCTGAACATAGTGCAACTAAATGCATTGGGATGACAATTGAAACgtgagttcgatgcagtaatcatgtacaacatctaaatttgaaatctgtcttttttgcctcaatgttttctcta-aaagccttcatagtatctatatattga--------------------------------

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 3
TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaag--atcatttgacaa-tctaaactacccatatgcttaggttccttgatggttctgtatgatttccccatgaaacatctttattaacttcagttctataaactattgttgtctttcctcaaaattacag
| |||||||| || || |||||||||||||| ||||||||||||||||||   || ||||| ||| ||||| | || |||||||| ||||| ||||| |||| ||  |  ||||| |   | | || |    ||   | |    | | |     | ||| |  |||   |   |  | ||    |||  ||  | || | |                               
TACATGATGCTTTGTCAGGACACACTTCTGCCAATGTTGAAGAGGCTGTTGCCTACTCAGAGCATAGTGCAATAAAGTGTATTGGAATGACCATTGAAACgtgagttactatttgccctctttgaaatgggaattcacatcatcttcatccctatgctgaac-attggtcttagttagattcaaatttcctataattttct-------------------------------

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|29666830|gb|CB663105.1|CB663105
EST:     TGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGAC                         GAGACCTGATTATTGCTTGGGGCCTCATTTGCGCCAGATGCTATCTTAT
genomic: TGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaagatcat ... aaaattacagGAGACCTGATTATTGCTTGGGGCCTCATTTGCGCCAGATGCTATCTTAT




















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: 74 (upstream exon), 75 (downstream exon)
Score: 33

TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaagatcat ... aaaattacagGAGACCTGATTATTGCTTGGGGCCTCATTTGCGCCAGATGCTATCTTATGGTTGTACCCGCTTAGAAATTGGTGTTCAGAGCACATACGAGGATGTTGCA




<











<


<