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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatacacacatgaacactggaagccccaagtcggccttttacttctattagttttattaatgtcttttttttctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
gtatatacacacatgaacactggaagccccaagtcggccttttacttctattagttttattaatgtcttttttttctgtt---acagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA
||| ||      ||   || ||      ||| | |    |||   ||  | ||  | | || ||| ||   | || ||||   |||| | ||||| || ||||||||||| || | ||| ||  ||| ||| || ||| | ||||||||||| ||||||||||| || |||||||||||||  || |
gta-attgttttattgccattga-----ccatgccattttttccttttgaatatgtcttttgatgactgaatcttgtgtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
--gtatatacacacatgaacactggaagccccaagtcggccttttact-----tctattagttttattaatgtcttttttttctgtta--cagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA
   | | |  ||   ||     |     |  ||| |      ||   |     | || |  | |  |||   |||  |  || | | |  ||| | ||||| || || |||||||| || | ||| ||  |||  || || ||  | |||||||| |||||||||||||| || |||||||||||||  || |
gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
---gtatatacacacatgaacactggaagccccaagtcggcct-------tttacttctattagtttt---attaatgtcttttttt------tctgtta--------cagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA
    | | | |     |  |      ||      ||||    |       || ||||  ||    |||   | | |||  ||||  |       ||||||        ||||| || || || |||||||||||||||| ||||||  |||  ||||| ||| |||||||||| |||||||| ||||| || |||||||||||||  || |
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 12
---gtatatacacacatgaacactggaagccccaagtcggccttttacttc-tattagttttattaatgtcttttttttctgtt----acagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA
    | ||| ||||     | | || |||       ||  | |||   ||  | ||| | |||| ||| |  | | | |||||     |||||| || || || ||||| ||||| || | | | ||  | |  ||||| ||  | |||||||| |||||||||||||| || |||||||||||||  || |
gtaatttattcacaagcatagattgtaagttttctttctacttttattttaatcttattcttatcaatattatatctgtctgtatccaacagCTACCCCAGACAAATCCCGGATTCAACAACTCTCCATTCAAATTTACAAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

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|86899049|gb|CI296221.1|CI296221
EST:     AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG                         CTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
genomic: AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
EST: gi|89163644|gb|CI100534.1|CI100534
EST:     AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG                         CTCCCACATACCCATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
genomic: AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
EST: gi|88223226|gb|CI223075.1|CI223075
EST:     AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG                         CTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
genomic: AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
EST: gi|29639377|gb|CB644386.1|CB644386
EST:     AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG                         CTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
genomic: AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
EST: gi|8955595|gb|BE229401.1|BE229401
EST:     AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG                         CTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
genomic: AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
EST: gi|86260523|gb|CI066396.1|CI066396
EST:     AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG                         CTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
genomic: AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
EST: gi|86504086|gb|CI146719.1|CI146719
EST:     AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG                         CTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG
genomic: AAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAG

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: 68 (upstream exon), 64 (downstream exon)
Score: 20

GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAGgtatatacac ... tctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtcggccttttacttctattagttttattaatgtcttttttttctgttacagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA
                            tattaat  putative branch site (score: 20)
                                  tgtcttttttttctgt  CT-rich tract
          ttttacttctattagt  TA-rich tract