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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtttgaacatcttttctgactgacgatattgacataattccatttagttagtatactactgtcattatattattgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG

Basic information

species Oryza sativa
transcript LOC_Os12g30540.1
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
----------------------------gttcgtttgaacatcttttctgactgacgata-ttgacataattccatttagttagtatactactgtcattatatt-attgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG----------------
                            |  | ||||| |   | |  |||   |  | |  | |  ||  |  ||| |  |   ||||| ||||     | |  ||||   ||||| ||| |  ||  |    ||||||||||| ||||||||||||||||| |||||||||||||| || |||||||||||||| ||||| |||||||| |||||||| ||||||                
gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacactactgtcaatt-ttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 17
--------------gttcgtttgaacat--cttttctgactgac--gatattgacataattccatttagttagtatactactgtcat-----tatattattgatttgcataacatttttgctaccaatt--gaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG----------------
               ||   ||||   |  |  |||   ||      | |   | | ||||  |||||   || || |  |||| ||     | ||   |||  |||||||||| |    ||  |||||  | ||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || |||||                 
gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaag-attcatctgtgatacttatgtaaagttgtcttgcataacactgcatctgtcaattttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 23
-gttcgt-ttgaacatcttttctgactgacgatattgacataattccatttagttagtatactactgtcattatattattgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG
  || || || ||  || |||    ||| | ||  ||  |||  |   ||    | | | | || |  |||    || |  | || |||     ||    | || ||||   ||||| || || |||||||| ||||||||| | |||||||||||||| |||||||| |||||| |||||||  | | ||||||||||
cttttgtcttcaatgtcatttt---ctgtctatggtgttatacattttttcg--tggcacattatt--cat----ttttcaagtttcat----cttcaatttcctattgctgcagATTCCTGAAGAAGAGAAAAACCTTGGCTCGCATGATCGGTTGATCCATGTTTATCATTTCTTGAAAGACACAACTCAAAATCAG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
--------------------------------------------------------------------------gttcgtttgaacatctttt---ctgactgacgatattga---cataattccatttagttagtatactactg-tcattatattattgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG---
                                                                           || |||  ||      |    ||| | |||  |  | |    ||||||   ||   ||  | | | | |  |||  | || |||| | | | || |||  |      ||| || ||||||| ||||| |||||||| || |||||  | ||||||||  | |||||||||||||||||||  |||||  |   |||||| ||    
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattctta-catggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 27
gttcgtttgaacatcttttctgactgacgatattgacataattccatttagttag-tatactactgtcattatattattgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG---
                    |||     ||  || | ||   |  |   |  ||  | ||||  |||  | || ||    | |   ||       ||  |   |||     ||||| ||||| ||||||||||| ||||| || |||||||| ||||||||||||||||| ||||  || ||  ||   || ||||||   
-------------------ttgatcattgaactttagatcgatgtacacaaatatctttactggtgttctcatgttggctaatcttatcttgaactt--ttttaatcatctcagattccagAAGAAGAGAAGAATCTTGGTCCCCATGATCGCTTGATTCATGTTTACCACTTCACAAAGGAGACTGTACAGAATCAGATG

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 27
gttcgtttgaacatcttttctgactgacgatattgacataattccatttagttagtatactactgtcattatattattgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG---
  |     || || |  | |    ||||  | | ||| | |||    |||  ||| | |  | |   |   | | |   | ||   |||| | |||        ||   |||||| || || || ||||| ||||| || || ||||||||||||||||||||||| ||||| ||||||||  | | ||| ||||||   
--ttaccagatcaaccatccactttgactctttagacctgattg---tta--tagcaaatcagtaggagggtttcaagtagttttttaacttgtttct------ttactacagATTCCTGAAGAGGAGAAAAACCTAGGTCCTCATGATCGGTTGATTCATGTTTATCATTTTATGAAAGACACAACTCAGAATCAGGTG

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|58678315|gb|CK067002.1|CK067002
EST:     AGAAAATAGAGAACATAAATGATCAGTACTGGACACTACGTGCTGAGGAG                         ATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTT
genomic: AGAAAATAGAGAACATAAATGATCAGTACTGGACACTACGTGCTGAGGAGgttcgtttga ... attgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTT




















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: 66 (upstream exon), 74 (downstream exon)
Score: 38

ATATTTCCACCTCACGAGAAAATAGAGAACATAAATGATCAGTACTGGACACTACGTGCTGAGGAGgttcgtttga ... attgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actactgtcattatattattgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG
                         gcataac  putative branch site (score: 38)
         attatattattgattt  TA-rich tract