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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

Basic information

species Oryza sativa
transcript LOC_Os03g09250.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
-tagttccag--tctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
 | |||   |  |||  ||||| ||| ||| | ||||||| |  ||| ||   || | |  |  | |  |  ||  |||   | | | |    | | ||| |||||||| ||||| |||| ||||||||||||||| || ||| |||||||||||||||||||||||||||||||||| |||| ||| ||||| |||||||||
atggtttggggatctagattaacatgattgaagcaacatggctcactggta--tacgtaatccatta-tagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
---tagttccag--tctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
   | |||  |   |||  |||||  |||||| |  || |||    ||| ||   || | |  |  | | ||  ||  |||    || | |   || | ||| |||||||| ||||| |||| ||||||||||||| | || ||||||||||||||||||||||||||||| |||||||| || | ||| ||||| ||||| |||
acatggtttgaagatctagattaacgtggttgaagaaatatggttcactagta--taagtaatccatta-cagaagctatggc--ttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
         | ||   ||      |    | | ||| ||| || |      ||  ||| | |  |  |||  || | | |   | ||   |   |   |||| ||| ||||||   | |||||||||||||||||| ||  |||||||||| ||||| || ||||| |||||| |   ||| || || |||||||| |||
------gtatatgtcctatttcaatctacata-cat-acatacatacatacatacatgatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------------------tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaa-acattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                                                                                | || |  |||||  ||| ||      ||     |       |  |||   | | |  |  || ||| |    || ||     |||||  | | || |||||||||||| || || | ||||||||| || ||||||||  ||||||| |||||||| ||||| |||||||||||    ||||| || || ||||| | |
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttg-ataatgaaaattttaaaaat-aattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgat-attttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                                  || | |  |||         |||    ||   | |     |  | || | ||| | || ||   ||||||||| ||||| |||| ||||||||| ||| |||| ||||| |||||||||||||| ||  | || ||||||||   ||| || || || || || | |
--------------------------------gtat-atagtcttacatagcaaaattagttagttagttagtgtattgatgtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 4
tagttccagtctgcattaagatggttggaacaacat-gacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                     |  || |   ||  | ||   | || |  || |     || |   | ||   |||| | |   ||| ||  |||    ||  | ||||||  | | | |||||||||||| || ||||| ||||||||||||||||| ||| | |||||| ||||   ||| || || |||||||| | |
--------------------gtacttcgtcgaatctcgattgagttcttcctct-----cttt---cttttctcatgttttcgctttcatccctt--gcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG

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|29646112|gb|CB651119.1|CB651119
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGANCA-GGTGGTGGTGTTGTGGACTG
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGA-CAAGGTGGTGGTGTTGTGGACTG
EST: gi|58598823|gb|CK009351.1|CK009351
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|3760166|gb|C97424.1|C97424
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|59930133|gb|AB178675.1|AB178675
EST:     TCAYGGGCACCAAGACGGAGCAGATGGAGCAGATCATACA-GGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: TCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCAT-CAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|13420717|gb|AU174807.1|AU174807
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|58675021|gb|CK063708.1|CK063708
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|58598555|gb|CK009083.1|CK009083
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|218487632|gb|FG964358.1|FG964358
EST:     CCAAGAAGGA-CAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAATGTGGTGGTGTTGTGGACTGC
genomic: CCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|29616445|gb|CB621457.1|CB621457
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                                  ttttttttattactt  CT-rich tract
                taaacattagacatga  TA-rich tract