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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttgaagtaattatattatcaattggattgtattgtttctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC

Basic information

species Oryza sativa
transcript LOC_Os06g09290.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
ttccacatatgttgtttgcat-tgcacttgt-gtgatgctgttcttgaagtaattatattatcaattggattgt------attgtt-tctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
         | ||| ||   | | ||  ||| ||| |  | |||  |||  | ||  | | |   |    | ||      | | || |||||     |   |  | ||| |||||||| ||||||||||| |||||||| ||| | |||||||| ||||| || || |||||||||||||||||||| ||||| ||||||||||| |||
---------ttttggttatttctccatgtgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
-----ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttgaagtaattatattatcaattggattg--tattgtttctcatcctgtgtatcat-acagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
     || |  ||| ||  ||||   ||||    | |  |   |       || ||   | |   ||  | |  ||  | |  |||  | | |  | ||||||  ||| |||||| ||||||| || || ||||| ||||||||||| || || |||||||| || || ||||||||||| || ||||| || ||||||||||| || 
gtatgtttccaataagtaatttga--tgcaagaatatt-tatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
-------------ttccacatatgttgtttg--cattgcac-ttgtgtgatgctgt--tcttgaagtaattatattatcaattggattgtattgtttctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
                 || | || ||||     ||| ||  ||| | || |  |   | ||  |||  |||| || ||   | |  || | ||    |||| |  |  ||  | ||| |||||| ||||||| || || |||||||||||  |||| ||||| ||||| || || |||||||||||||| || ||||| || || |||||||| || 
gtatgttccaatcagtaacttttgatgttaaaatattccatgttgagagaagaaggggtattctagtg-ttatgttgtctgcttgtctg-actgaacttcattccat-cat--ttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 5
-------------ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttgaagtaattatattat-caattggattgtattgtttctcatcctgtgtatcata-cagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
                 || | || ||||   ||    | ||| |||          |   |  |  | |||| |  |  | |||| |   |   | || | || |||||  ||| |||||| ||||||| || || |||||||||||  |||| ||||| ||||| || || |||||||||||||| || ||||| || || |||||||| || 
gtatgttccaatcagtaacttttgatgttaaaatattccatgt-tgagagaagaaggggtattctagtgttatgctgtctgcttgtctgactgaacttcat-tgcatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCTAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
------ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttga-agtaattatattatca-attggattgta--ttgtttctcatcctgtgtatcat-acagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
       |||| ||| ||  ||||         ||| | |   |       | || || | |||   |   ||| ||  |   ||||||  | | |  | ||||||  ||| |||||| |||| || || || ||||| ||||||||||| ||||| |||||||| || || |||||||||||||| ||||| || |||||||| || || 
gtatgcctcca-ataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 5
ttccacatatgttgtttgcattgcacttgt--gtgatgctgttcttgaagtaattatattatcaattggattgtattgtttctcatcc-tgtg-tatcat-acagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
      ||   ||    |   || ||||     | ||  |  |  ||||  ||||   || |  | ||  || |  | | ||||| |    || |  |||  ||| ||||||||||| || || || ||||||||||| ||||| |||||||||||||| || || ||||||||||| || ||||| ||||| |||||||| || 
-----gatgcctttaaaggcatgtacttcctcataatttttgtggtgaaaaaatttatttgtttaatgtgttcttgtttgtctcaccaacatgctgccattgcagGGTTGATCGAAATAAATATCAGATTCAAATTCCCTTGCCCCCAAAGATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATAT

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------ttccacat----atgttgtt-tgcattgcacttgtgtgatgctgttc---ttgaagtaattatattatc-aattggattgtat-tgtttctcatcct-----------gtgtatc-atacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
                                              |   | ||    || ||| |     |  ||  | | |     ||||    |||  |||| | | ||| | |  |  | || || || |||| | | |            | || |  | ||| || || ||||||||||||||||| || |||||  ||||||| |||||||| || || || || |||||||| || |||||||| |||||||| || |||
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttcttaactttattagttataatatacctgtgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------ttccacatatgttgt-ttgcattgcacttgtgtgatgctgttcttgaagtaattatattatcaattggattgtattgtttctcatcctg-tgtat-catacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
                                                                                                 |  || |  ||| |  |||| |      |   |  | || |  | ||    |  |||| |      |||  ||   |||    || |  | ||    | ||| || ||| |||||||||| ||||| || ||||| ||||| || |||||||| ||||||||||| |||||||| ||||| ||||| |||||||| || |||
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 5
ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttgaagtaattatattatcaat-tggattgtattgtttctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
                                  |   ||| ||    |  |||| || || || |  ||   |||  |     | || |      ||||| |||||| | ||||| || || || ||||| |||||||| || ||||||||||| ||||| || |||||||| ||||| || || || ||||| ||||||
---------------------------------gtatggttttt----ttcttatgttctcgatgtaaatgacatttctgtgtgttctat------tacagTGTTGATAGGAACAAATATCAGATCCAAATACCTTTGCCCCCTAAGATTGATCCGAGCGTCACTATGATGACGGTGGAGGAGAAGCCCGATGTAACTTAC

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|58586381|gb|CF984689.1|CF984689
EST:     TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGG                         AGTTGATCGAAACAAGTACCAAA
genomic: TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGGgtaggtttct ... tatcatacagAGTTGATCGAAACAAGTACCAAA
EST: gi|58653641|gb|CK042321.1|CK042321
EST:     TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGG                         AGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGA
genomic: TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGGgtaggtttct ... tatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGA
EST: gi|58658676|gb|CK047356.1|CK047356
EST:     TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGG                         AGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATGGA
genomic: TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGGgtaggtttct ... tatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGA
EST: gi|29666226|gb|CB662501.1|CB662501
EST:     TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGG                         AGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGA
genomic: TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGGgtaggtttct ... tatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGA
EST: gi|58592633|gb|CF990941.1|CF990941
EST:     TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGG                         AGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGA
genomic: TTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGAATGCGGGTTGGgtaggtttct ... tatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtaattatattatcaattggattgtattgtttctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC
     attatattatcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttgaagtaattatattatcaattggattgtattgtttctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - atgttgt
- - - - - - - - - cattgca
- - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - gttcttg