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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttggtttcatcaaccttgcttcctccataacatatgcatacctgctgattatctgttaattttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG

Basic information

species Oryza sativa
transcript LOC_Os06g03760.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 11
tttgttggtttcatcaaccttgcttcctccataacatatgcatacctgctgattatctgttaattttctcc--actaagaggccat--ctaaaatcttt-tgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
|||| | | || ||     |||  | ||        | | | ||  |  ||||       | || ||   |  ||||  |  |  |  ||   || | | |||||||||||||||||||||||||| |||||||| |||||||| ||||||||||| ||||| |||||||||||||||||| ||||||| || ||||||||||||
tttgattggtttat-----ttggctgctgagctttgtcttcgtatttcgtgatcgaaaaatcatcttaatctaactaccatacttttcctgccatatgtgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
tttgttggtttcatcaaccttgcttcctccataacatatg-catacctgctgattatctgt-taattttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
    |  || |   |  |||   ||  || |   || ||  |||    |     ||||  | | | | |    |  |        |   |     | |||||||||||||||||||||||||| |||||||| || || || ||||||||||||||||| ||||| |||||||||||  ||||||| || ||||||||||||
--catgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 11
--tttgttg-gtttcatcaaccttgcttcctccataacatatgcatacctgc-tgattatctgttaattttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
  |  |||| |||  ||  |   ||     |  ||        |||       | ||  | || |||  ||    |      ||   | | |   | ||| ||||||||| ||||||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || |||||||||||  || ||||||| ||||||||||| 
actaagttgtgttctatacatagtgaaaaatt-atggtgctgtcatgataatgtcatgctgtgataacattgctgaaagttcggttgtttta---ccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAA

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
tttgttggtttcatcaaccttgcttcctccataacatatgcat-acctgctgattatctgttaattttctcca-ctaagaggccatctaaaat-cttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
  | | |     |       |  ||    |||||   |    | |  |  | || ||    | ||  | | || || | ||  |   |    | | ||| ||||||||| ||||||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || |||||||||||  || | ||||| || |||||||| 
--tatagcgcatagtg-ttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
tttgttggtttcatcaaccttgcttcctccataacat--atgcatacctgctgattatctgtta-attttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
  |      | |||   |  | | |  |  | ||      ||| | | || | ||    || |    |  |  |  | | ||  ||  |     | ||| ||||||||| ||||||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || |||||||||||  || | ||||| ||||||||||| 
--taccaagt-catgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
tttgttggtttcatcaaccttgcttcctccataacatatgcatacctgctgattatctgttaattttctccactaagaggccatctaaaat-cttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
    || || |  |  |    || |    ||     ||||    | || | ||    || |      |    || | ||  |   |    | | ||| ||||||||| ||||||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || ||||| |||||  || | ||||| || |||||||| 
-cacttagtgttctatataaagcgtaaggcacttgttatgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
-----tttgttggtttcatcaaccttgcttcctccataacat-atgcatacctgctgattatctgttaattttctccactaa-gaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
      || || |||     |       |      ||| ||| |    ||  |  | | | | | ||  |    || ||||  | |||   || ||||      |||||||||||| ||||| ||||| || ||||  |||||||| ||||| || || ||||||||||| |||||||||||  |||| || || || || ||||||
gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaact-tttattcttacaatcgactattgtggctcactgaaattc----cagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 11
tttgttggtttcatcaaccttgcttcctccata-acatatgcatacctgctgattatctgttaattttctcca-ctaagaggc-catctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
  | || | |   |||| |        |  ||| |||  |||   |||    ||||  |||||||  || |   || ||         | |  |    ||||| |||||||| || |||||||| || ||||  ||||| || ||||| ||||| || |||||||| |||||||||||| |||| || ||  | |||||||||
-ctattagat--gtcaaaccaagacttttaatatacagctgctaccctcacaattacatgttaatcctcacagtctgagtaatgtggttcatttaaaatgcagCGTGATTCAATTTTGTGCCACTGCATTTGGATATTACGCTCAAGCCACTGCTGCCCAGGAGATATTTGGCCACACATTGCAGTCCCTTAGAGGAATTAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------------------tttgttggtttcatcaaccttgcttcctccataacatatgcata---cctgctgattatctgttaattttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
                                                               |  ||     | |   ||  ||  |  | || ||||    |   | || |   | | | |  ||  ||     |    |  | || ||      || |||||||||||| ||||| |||||||| |||| ||| ||||| ||||||||||| || ||||| || ||||||||||||||| ||||||||   |||||||| 
gtttgcatgtttagtcctctaaattcattaacagatataattgggttgggaccagcaccacaaggggggactcttactgttattttatgtagaatatatttccagaccttggtagatgtttatctataatcattgttgttggctcctccaa------tttcagTGTGATTCAATTCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAA

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|89176031|gb|CI043052.1|CI043052
EST:     TAATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: TAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
EST: gi|87019966|gb|CI299364.1|CI299364
EST:     ATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: ATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
EST: gi|58684950|gb|CK073637.1|CK073637
EST:     ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
EST: gi|86484582|gb|CI127215.1|CI127215
EST:     CTGTTGAATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: CTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
EST: gi|5667175|gb|AU077435.1|AU077435
EST:     ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
EST: gi|88961963|gb|CI097116.1|CI097116
EST:     ATGAACTCGTTCCTGTTTAATGTTGGACTCATCATACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
EST: gi|55827892|gb|AU063117.2|AU063117
EST:     ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAG-AACCTG
genomic: ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAAC-TG
EST: gi|89163461|gb|CI100351.1|CI100351
EST:     CCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: CCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
EST: gi|29679858|gb|CB676133.1|CB676133
EST:     ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAG                         TGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC
genomic: ATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAGgtgtgctact ... tcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgattatctgttaattttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
                                     atctaaa  putative branch site (score: 3)
                                             tcttttgc  CT-rich tract
      attatctgttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttggtttcatcaaccttgcttcctccataacatatgcatacctgctgattatctgttaattttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC