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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtttttttttccagcactacatgttgatgtgattagtattcgtaattggttgttatatttgagtgcttttttccttgaactaattattgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC

Basic information

species Oryza sativa
transcript LOC_Os05g51530.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 6
cttgtttttttttccagcactacatgt-tgatgtgatta-gtattcgtaattggttgttatatttgagtgcttttttcct-tgaactaattattgatt-tatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC
  |||      |  |   | ||  |   |||| |  |||  || |  || |    |  |  ||| || ||     ||| | ||| |||| || | |||  ||||||||| || || |||||||| || ||||| ||||| || |||||||||||||| || ||| | ||||||||||||||||||||||||||||||||||| |
--tgtcaaggctgtctaaattatgtacctgatttccttatatagttatattca--tacttgattcgactgtcccattcatatgagctaactaataattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G128995_T02 (Zea mays), 3'ss of exon 4
cttgtttttttttccagcactacatgttgatgtgattagtattcgtaattggttgttatatttgagtgcttttttcctt--gaactaattattgattt-atagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC
   ||     ||  |   | ||  |       |   | ||||   ||  |   |     |||||| |||     | | |  || |||| |    |||| ||||||||| || || |||||||| || ||||| |||||||| |||||||||||||| |||||| |||||||||||||||||||||| |||||||||||||| |
---gtcaacgttgtctaaattatgtccctgacttccttgtatagttatattcataccggatttgactgcccccattcatatgagctaactgaaaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G177912_T01 (Zea mays), 3'ss of exon 7
cttgtttttttttccagcactacatgttgatgtgattagtattcgtaattg-----gttgttatatttgagtgcttttttc--cttgaactaattattgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC
      | |   ||||| |  | | ||  |    |||   ||| |  |  |     ||  |||   |  ||      ||||  ||||| ||||  ||   |||||||||||| || || |||||| | || ||||| ||||||||||| || ||||||||  ||||| | ||||||||||||||||||||||||||||||||||| |
------tatgaatccagtaa-aaaggtaaaacaaattttaatttgggacggagggagtatttagtatcaagcagccctttcatcttgagctaaacatgattttatagGTACCCAGGTCATCTAAACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 6
cttgtttttttttccagcactacatgttgatgtgattagtattcgtaattggttgttatatttgagtgctttttt-ccttgaactaattattgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC--------
            |  |    || |      | | ||| |     |     |  | |  |||      ||  |||   ||||| ||||  ||   |||||||||||| || || |||||| | || ||||| ||||||||||| || ||||||||  ||||| | ||||||||||||||||||||||||||||||||||| |        
---------cagtaaaaaggtaaaacaaattttaatttgggacggagggagtatttagtatcaagcagccctttcatcttgagctaaacatgattttataggtacccagGTCATCTAAACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAG

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|29656670|gb|CB652945.1|CB652945
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|29662007|gb|CB658282.1|CB658282
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACGATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|29612869|gb|CB617882.1|CB617882
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|58666270|gb|CK054956.1|CK054956
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|218479849|gb|FG959490.1|FG959490
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|29674593|gb|CB670868.1|CB670868
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|25802832|gb|CA758793.1|CA758793
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|29613101|gb|CB618114.1|CB618114
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|38565596|gb|CK085049.1|CK085049
EST:     AAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: AAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
EST: gi|29613962|gb|CB618975.1|CB618975
EST:     ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTG                         GTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC
genomic: ACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatat ... tgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattggttgttatatttgagtgcttttttccttgaactaattattgatttatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC
                                ttgaactaattattga  TA-rich tract