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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT

Basic information

species Oryza sativa
transcript LOC_Os01g05800.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G839422_T01 (Zea mays), 3'ss of exon 7
gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatccttttttt-ctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
          |   | | ||||  || | | | |||| ||| ||| ||||| | || |   |  || |||||     | ||||   |  | | |  ||||  ||||| ||||| |||||||||||| ||||  ||||||||||||||||||||||||| || |||||||||||||||||||| ||||| ||||| ||||
--------gtggatgcttctctgtat-attctttcatttgttatagtgccaat-tatacattgcga-tggcttaacttgtgatttatggtctgccacagAGCGATGACCCATCACAGAAGAACACAATGCTCATTTTGAAATTTCTTCCATTTATGATTGGCTGGTTCTCTTTGTCAGTGCCATCAGGATTGTCTATTT

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G110063_T01 (Zea mays), 3'ss of exon 8
gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
          ||  | | | ||  || |   | || |  || ||  ||||| | |||| | | | |    ||    || |     |  | |    |||| |||||| || || |||||||||||||| || |||||||||||||||||||||||||| || |  ||||||||||||||||| ||||| ||||| ||||
--------gtgaatgcttccctgtat-atcctttcgttggttatgatgccaat-tacatggtttaa----cttaagatcta----tggtctggcacagAGTGATGACCCGTCACAGAAGAACACACTCCTCGTTTTGAAATTTCTTCCATTTATGATTGGCTATTTCTCTTTGTCAGTGCCATCAGGATTGTCTATTT

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 7
gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
                 |     ||| | | |||  ||||     || |  || |    | |             |||| | |  |||||||  |||||||||||||||||| || ||||| ||||| |||||||| || ||||||||| | ||||| || |  || ||| | || || || ||||| || || ||||
-----------------gtaaagaataagtctattttctgatcattttcttctctttttgtttcattcctagtaaaattgggtttttttttttggcagACTGATGATCCATCTCAAAAGAATACACTTCTTGTTTTCAAGTTTCTTCCACTCATGATTGGTTACTTTTCTCTATCTGTCCCATCAGGATTATCAATTT

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|29615536|gb|CB620548.1|CB620548
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|66920591|gb|CX107439.1|CX107439
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAAC-CACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|29620327|gb|CB625339.1|CB625339
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|58694651|gb|CK083338.1|CK083338
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|38482468|gb|CF966504.1|CF966504
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAGATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA

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: 73 (upstream exon), 75 (downstream exon)
Score: 47

TCCTCCATTAGGCTGGCATGACACGATATGTTATCTTGTGTTGCCTGTGCTACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
                                 atttgat  putative branch site (score: 47)
                                  tttgatcctttttttc  CT-rich tract
                                          tttttttct  TA-rich tract