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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataacactggaatatgcgcttaatgaaattcttaaaacatgtagcattgccagcaatataaatttcttgcataatttaattgatttcatgtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGAGTCTGATGTCAAAAACTGCCTGGAGATATTTGCTACTAGCTGGATAAGA

Basic information

species Oryza sativa
transcript LOC_Os12g35570.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g35570.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 10
----gataacactggaatatgcgcttaatgaaattcttaaaacatgtagcattgccagcaatataaatttcttgcataatttaattgatttcatgtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGAGTCTGATGTCAAAAACT-GCCTGGAGATATTTGCTACTAGCTGGATAAGA-
    |                  || ||||||| |   | ||   |   |||         ||| |||||| ||||    ||    ||||   | ||||||||||||||||||| ||| ||||| | ||| |||||||||||||||||||||||||  | | | | | |||| |     | || |||| ||  ||  ||| ||   
ttttgtagttgtcacttcccagactgaatgaaact---ataatcggcctcatgtgagtttgtatgaatttcctgcaatgctttgacgattctgt-tttgtgcagATGGTCGATGCATTCATGGCAGTGAGGCCTCTTCCCAATATGTTTGGCTGAGCATCACGGCGACAACTTGAACAAACATTTTTGTTATCAG--GGAGAATTT
















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|88960314|gb|CI382192.1|CI382192
EST:     CCGAACTGGTTGCGAAACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAAACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|86413378|gb|CI067783.1|CI067783
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|86432592|gb|CI086203.1|CI086203
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88248644|gb|CI248493.1|CI248493
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88317508|gb|CI672084.1|CI672084
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|86426525|gb|CI071622.1|CI071622
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|86883703|gb|CI328731.1|CI328731
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|89195763|gb|CI007182.1|CI007182
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88262215|gb|CI365791.1|CI365791
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|86434156|gb|CI094499.1|CI094499
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|86598581|gb|CI355198.1|CI355198
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|89191021|gb|CI392874.1|CI392874
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|86538796|gb|CI179002.1|CI179002
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88269434|gb|CI380732.1|CI380732
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88270262|gb|CI385520.1|CI385520
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGAT-TATTTATGCCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88288817|gb|CI517948.1|CI517948
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88272557|gb|CI386412.1|CI386412
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|29674926|gb|CB671201.1|CB671201
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|89162323|gb|CI104651.1|CI104651
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
EST: gi|88269034|gb|CI380332.1|CI380332
EST:     CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAG                         ATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA
genomic: CCGAACTGGTTGCGAGACATCAAAGAGCTAGAGCACTAGTGACCGAGGAGgtacacaact ... gtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgccagcaatataaatttcttgcataatttaattgatttcatgtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGAGTCTGATGTCAAAAACTGCCTGGAGATATTTGCTACTAGCTGGATAAGA
                                 aattgat  putative branch site (score: 4)
          aatataaatttcttgc  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataacactggaatatgcgcttaatgaaattcttaaaacatgtagcattgccagcaatataaatttcttgcataatttaattgatttcatgtttgtgcagATGGTCGATGTATTTATGGCGGCGAGACCTCTTCCCAATATGTTTGGCTGAGTCTGATGTCAAAAACTGCCTGGAGATATTTGCTACTAGCTGGATAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA