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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG

Basic information

species Oryza sativa
transcript LOC_Os06g11180.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 17
----gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG
     | ||  ||||||| || | | | || ||| | |||   | ||  ||||  | |||| ||| |     ||||||          ||||   |||| |||||| |||||||||||||| || ||||||||||||||| ||||||||||  ||||||| ||||| ||| ||||||||||||||||||||||||||||||| |
gttgttgcctcactgtat-acctatgtttc-atattttcagcaccctcgacactatcaacc-tgc-acggacttgtgac----ctctttcttgattttggacagGCGGAGAACATCAAGTTCACCTTGGAGCAGCAGATGTTGTTCTTTGCAAGATTAGTTGGGAAGTTTGAGGTGGCAGATGATATAACTCCAATCAAGATTG

upper sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 17
gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttga-acagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG
                            ||  | | | | |  |||     ||     |   || |  | ||||  |       |  |   || ||  |||||||||||||| ||||||||| | ||||| || ||||| |||||||| ||||| || ||  | || || || || |||||||| | ||| ||||| || |
---------------------------gtatgcgccaatttaattat---ttatcttttagaatgaaatagtgaatgtaatcaataatgggttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG

upper sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 17
gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataag-gttgtgatggagtatgctcttccatttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG
          ||||   || ||| | | |  |||  | || | | |     | |    || | |||   ||   ||  |  |   | ||    ||  | ||||||| || || || || || |||||||| || ||||| ||||||||||| ||||| ||  | || |||||||||||||| || ||||| ||||| ||||
----------gtatgtattatctatgttttatct--aatcacataa--tttttatttttgaggtaaatattagaattaatcaaattgtt----ttacatagGCTGAAAATATTAAATTCACATTGGAGCAACAAATGGTATTCTTTGCTCGTTTAGTGGGACACTTCAAGGTGGCAGATGAGATTACTCCCATCAAAATCG

upper sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 17
gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG
          ||||      | ||| | |    || |  | |   |     ||        |  ||  ||   |   |  |      |   |||  ||||||||| ||||||||||| ||  ||||||| || |||||||||||||||||  |||| ||  | ||| | ||||| ||| | || ||||||||||| || |
----------gtatttgcaatttctatgtttaatctaagcacgaaat-ttatatttatgagggaaacattagtactaatcagataactt--tttacacagGCTGAAAACATCAAGTTCACACTGGAGCAACAAATGGTGTTCTTTGCTCGTGTAGTGGGACACTTTGAAGTGGCGGATCAGATTACTCCAATCAAAATTG

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|86412718|gb|CI067123.1|CI067123
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
EST: gi|88903654|gb|CI089192.1|CI089192
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
EST: gi|13805721|gb|AU181175.1|AU181175
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
EST: gi|86479713|gb|CI122346.1|CI122346
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGGACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
EST: gi|29630392|gb|CB635401.1|CB635401
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
EST: gi|29630391|gb|CB635400.1|CB635400
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
EST: gi|12622658|gb|AU172871.1|AU172871
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
EST: gi|86479598|gb|CI122231.1|CI122231
EST:     TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAG                         GCTGAGGACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA
genomic: TGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCCGCAAGgtaccaaact ... atttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG
   ccctaaa  putative branch site (score: 3)
                                      ctcttccattt  putative PPT
                                             atttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttgaacagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG