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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g70960.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G06700.1 (Glycine max), 3'ss of exon 5
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
|| |  || |  | ||| |   ||| |  | |   | | ||||| || | |    | || || |    |   |  ||     |||||||||| | |||||||| ||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||||                            
gtaatgctaattatttgat---agtaatgtctttggaattttctaatgtatg---tctacctgaaatatatatccttgtgatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGTGACCCACCTGCTGGTGTTTCG----------------------------

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
|| |       |   ||||   |    | |  | |    | | |    | || ||  ||  |||   |||    || |  |   |||||||  | |||||||| ||||||||||| ||||| ||||| |||||||||||||| || |||||||||||||||                            
gtaatgagtgtagtctgctagtaacgtctttagattt--tcttttgcttttatatcataaataat--tttacccttaatgt---ttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG----------------------------

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
|| |       |   ||||   | |    |  | |    | | |    | || || | |  |||   |||    || | ||   |||||||  | |||||||| ||||||||||| ||| | ||||| || ||||||||||| || |||||||||||||||                            
gtaatgactgtagtctgctagtaatgtttttagattt--tctattgcttttatatcggaaataat--tttacccttaatat---ttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGTGACCCTCCTGCTGGTGTTTCG----------------------------

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
|| |  || |  | ||| |   ||| | || |  || |||||   |      |  |   |  || | | | |  |||  || |||||||||| | |||||||| ||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||                             
gtaatgctaattatttgat---agtaatatctt-tgaaattttctaatgtatgtctacctgaaaatatatatccttttgat-ttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCA----------------------------

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgt-atctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
||  |   | |   ||     || |   ||    |   |    ||||||    | | | ||||||    ||  |   ||  |  || |||||  | ||||||||||| || ||||| ||||||||  | ||||||||||||||||| ||||||||  |||||                            
gtttggtgctct--ttctctccatttgtatacaattagaaaattcatct----actatgatctaagcaatt--tggctattttcttccagGCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCG----------------------------

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
  |  | |   |  ||   ||  |   | | |  || |  || |  ||| |    |  |  | |    ||| ||||    | |||||||||  | |||||||| || |||||||| ||||| || || |||||||| |||||||||||||||||  |||||                            
--gtaatttctatgttctggtttg--gcttcttatggagattat-gtctatgttatccaagtgatatcttgcttttg--ttcttttcagGCTCGCCACAATGGTCAAAACTATGTATTTGCACTGCTAACTGGTTACCGTGATCCACCTGCTGGCATTTCG----------------------------

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 3
--gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
   | |   |    |          |  | | |||       |   || | ||| |   || || |||||||||           | ||||||| | |||||||| ||||| ||||| ||||||||| | |||||||| |||||||| || |||||||||||                             
gtattaattttgttatagatcccttgatagaagtga-atggctgtccacccctaca--ataactgactctttgtc---------ctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA----------------------------

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|29669904|gb|CB666179.1|CB666179
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG
                        atctaac  putative branch site (score: 2)
                                              tattttc  putative PPT
                               tctttgttttttacat  TA-rich tract