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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatactcttaaaccttctgagtgaccgctggtgtccactcataagcagctagagtgacgcagtcacattgaagtactgatatgtttgcattctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG

Basic information

species Oryza sativa
transcript LOC_Os08g42410.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 5
gtgatactcttaaaccttctgagtgaccgctggtgtccactcataagcagctagagtgacgcagtcacattga-agtactgatatgtttgcattctg-ttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG
          ||||||| |      | | |   |||||| ||||||||    ||  |||| |   ||||||   | |||||||||  ||   || || ||||||| || || ||||| |||||||||||||| || || || |||||||| ||| | || |||||||||||||||||||| || ||||||
---------ataaacctgc----aaatcaccattgtccattcataagctatcaggttgacccgaccacattctcattactgatatcattttgttttggttcaggcgGGCTTCACTGGCATTGGTGTTGGTGCCGCTTACCATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 5
gtgatactcttaaaccttctgagtgaccgctggtgtccactcataagcagctagagtgacgcagtcacattga-agtactgatatgtttgcattctg-ttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG
       |  ||||||| |      | | |   |||||| ||||||||    ||  |||| |   ||||||   | |||||||||  ||   || || ||||||| || || ||||| |||||||||||||| || || || |||||||| ||| | || |||||||||||||||||||| || ||||||
------gttataaacctgc----aaatcaccattgtccattcataagctatcaggttgacccgaccacattctcattactgatatcattttgttttggttcagGCGGGCTTCACTGGCATTGGTGTTGGTGCCGCTTACCATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 5
gtgatactcttaaaccttctgagtgaccgctggtgtccactcataagcagctagagtgacgcagtcacattgaagtactgatatgtttgcattctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG
|     | ||| ||  |||  ||  |       ||     |  |    || | |  ||  || ||   |||||  || |  | |  |   ||    | |||||||| |||||||| ||||| ||||| ||||| ||  | |||||  | ||||| || ||||||||||| ||||||||||| ||||||
gcttctcactttaaaattcataggaaaataacatgattttttttttatagttggt-tgcagctgttggattgacataatttttttgtgaaatataatacagGCTGGGTTTACTGGGATTGGAGTTGGCGCTGCTTACTATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 5
-gtgatactcttaaaccttctgagtgaccgctggtgtccactcataagcagctagagtgacgcagtcacattgaagtactgatatgtttgcattctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG
  |  |    |||||  || |  |  |            | |  |    |  | |  | | || ||   |||||  || |  | |  |   ||    | |||||||| ||| |||| ||||| ||||||||||| ||  | |||||  | ||||| || ||||| ||||| ||||||||||| ||||||
gcttctcactttaaaatttgtaggaaaataagaacagg-atttgtttataattggtttca-gctgttggattgagataatttttttgtgaaatataatacagGCTGGGTTTGCTGGGATTGGAGTTGGTGCTGCTTACTATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtgatactcttaaaccttctgagtgaccgctggtgtcca--ctcataagcagctagagtgacgcagtcacattgaagtactgatatgtttgcattctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG
   ||  | ||||| ||  |     ||  |    || || |  || ||   ||  |    |||   ||     ||     | | ||  ||||        || ||||||| |||||||||||||| |||||||||||||||   ||  |    || || || || || ||||| ||||||||||||||||||
gtttggaattcttatactattatcttgtactgcagtctcaatccttatttccatgtttcttgattgagaagatttctgacagttat-cgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------gtgatactcttaaaccttctgagtgaccgctggtgtccactcataagcagctagagtgac-gcagtcacattgaagtactgatatgtttgcattctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG
                                 |    | | ||    | | |  || |    ||   |  |  || ||        | |    |  || || ||  |  ||   | ||||  |||  | | ||||||||||||||||| ||||| ||||||||||| ||  | ||||||   ||||| || ||||||||||||||||| ||||||||||||
gtaagttctgttacatgacttgcccatataagtggataagtttttgctcctttttgtaaattttgtgattaatccaaaaattttcttattattagtcgttactttctacaacatgtttgtt-acatattttgcagGCTGGTTTTACTGGGATTGGAGTTGGTGCTGCTTACTATGGTCTTAAGCCTGTTGTAGAGTTCATGACATTTAATTTCTCTATGCAG

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|428335|gb|D24483.1|D24483
EST:     TGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAG                         GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCT
genomic: TGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAGgtgatactct ... ttctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCT
EST: gi|218484233|gb|FG953202.1|FG953202
EST:     TGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAG                         GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCT
genomic: TGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAGgtgatactct ... ttctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagctagagtgacgcagtcacattgaagtactgatatgtttgcattctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG
                             tactgat  putative branch site (score: 2)
                                             ttctgttc  putative PPT
                                  atatgttt  TA-rich tract