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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC

Basic information

species Oryza sativa
transcript LOC_Os11g05700.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AC234203.1_FGT004 (Zea mays), 3'ss of exon 9
----------------------------------------------------------gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatgg---agccaccttattc---atagt----actaattgtga----tattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
                                                           |   ||  | |||| |||||        | | |             |  | | ||||||| | |  ||      |    ||||||    ||||    ||| | || ||    | || |  |||||||||||| ||||| |||||||||||||||||||| |||||||| |||||||| |||||||||||  | ||| | || ||  ||||||| || || |||||
gtaggactccttgctacacctgtactttgttttttcagaacccatagcaaattaaggaattctggaaggattttccattgacag-acacacactgaacacaacgttc-tatggtagcatgacatgtgttttgtcttgtttattctctgtagtctgtactgactgagagttttttttttgtatagTTGTGGAGGATGGCTCGAACTGGAGCATGGGTCAGAGGCAGCTCTTCTGTTTGGGACGTGCACTGCTAAGAAGATGCCGTGTCTTAGTCCTCGACGAGGC

upper sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G111903_T02 (Zea mays), 3'ss of exon 11
gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
       ||| |||   ||||| |         | | |  ||  || |  |  |  ||||| | | |||  |    || ||||      || | ||  || | ||  | |||||||||||||||| ||||||||||||||||||||||||||||| || ||||| |||||||||||| | ||| | || || ||||||||||||||||||||
------atgggattc-tcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacatatgaggttgtctaattct-----ctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC

upper sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G28900.1 (Glycine max), 3'ss of exon 11
gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
                           ||| |  |   |  |  |  |||   |||  || | ||| |       |||  || |||  |   | |   || |||| | |||||||| |||||||| || |||||||||||||| ||||||||  | || ||||| || ||||  ||||| ||  |  || | || || || || ||||| ||
---------------------------gtacactttcatcattatggtaactatgtcaca-agtactttt--tttcctagttgataaaaactagtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC

upper sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G28890.1 (Glycine max), 3'ss of exon 17
gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
                   | |  |||      | ||||     |  |||   | ||  ||   |          || | ||  || |  |   |  || ||||| |  ||||||| | ||| || || |||||||||||||| ||||| |||||||||||||| || |||||  | ||| |  |  |    || || ||  | ||||| ||
------------------gtgcacttt-----caactttcactattttaactatatataatgtaagcacttcttcccatgttagtaatgattcgtacgaaattgttacctagTTGTTGGAGAGGGATCAAACTGGAGCATGGGACAAAGACAGCTGTTCTGTTTGGGGCGTGCCATGTTGCGGAGAAGCAAAATATTGGTGTTGGATGAAGC

upper sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G28910.1 (Glycine max), 3'ss of exon 11
gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
                              |  | ||||  || |  ||   |       | | |  ||       | || |  || ||   | |   | ||||    | |||||| |||||||| || |||||||||||||| ||||||||  |||| ||||| || ||||| ||||| ||  |  || | || || || || ||||| ||
------------------------------gtaaactttcatcatcatatgataactatgtgacaagtgcttatttcctagttgtaataactagtaacaaattgatgcacagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTGTTTTGTTTGGGGCGTGCTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC

upper sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
             | || | ||||        | |||| |     |   || || ||| |    | |||            ||| |||  |  || |  | ||||  |||||||||||| ||||| || || ||||||||||| || || ||| |||||||||||||  | ||| |||||||| |  |  |  | ||||| || || || ||
------------gtaacaaatctt------agtttcttataagagagagat-ttctagtaagtcagatg---ttttgcggctcaaagttgtg-ttatatttttgtt-tatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC

upper sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv16s0050g02480.t01 (Vitis vinifera), 3'ss of exon 10
gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagta----ctaattgtgatattgtcatat-agTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
                                       |    |   ||  |  ||| | |  |    |  ||   || | ||| |||     ||||   | | |  |  | | ||||| ||||| ||| || |||||||||||||| || |||||||| |||||||| || ||||| || ||| || |  | || ||  | ||||||||||| ||
--------------------------------------gtaagatttcaagctcttagtaca-cagggtgtccctttttttccattgtagccattaataagggtctgtttgtttcagTTGCGGAAGGTGGATCAAACTGGAGCATGGGGCAGAGGCAGCTCTTCTGTTTGGGGCGTGCCCTCTTGCGAAGAAGCCGGATACTGGTTCTTGATGAAGC

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|29613678|gb|CB618691.1|CB618691
EST:     CCAACTTCTTGAGACTGTCCAAGAGAAGGAACATGGATTGGATTCACTTG                         TTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTT
genomic: CCAACTTCTTGAGACTGTCCAAGAGAAGGAACATGGATTGGATTCACTTGgtaggggtgg ... tgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTT
EST: gi|29687974|gb|CB684249.1|CB684249
EST:     CCAACTTCTTGAGACTGTCCAAGAGAAGGAACATGGATTGGATTCACTTG                         TTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTT
genomic: CCAACTTCTTGAGACTGTCCAAGAGAAGGAACATGGATTGGATTCACTTGgtaggggtgg ... tgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTT
EST: gi|33795959|gb|CF323847.1|CF323847
EST:     CCAACTTCTTGAGACTGTCCAAGAGAAGGAACATGGATTGGATTCACTTG                         TTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTG
genomic: CCAACTTCTTGAGACTGTCCAAGAGAAGGAACATGGATTGGATTCACTTGgtaggggtgg ... tgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTG

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: 72 (upstream exon), 54 (downstream exon)
Score: 15

GTTCTTGACAAATGCCAACTTCTTGAGACTGTCCAAGAGAAGGAACATGGATTGGATTCACTTGgtaggggtgg ... tgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
                              tactaat  putative branch site (score: 15)
                    ttattcata  TA-rich tract