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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaagacagctttacatgaactttcatttctgcatgcttccgcatttatttctgaagtcttcagatgaaaatttgccaacagagagaagttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT

Basic information

species Oryza sativa
transcript LOC_Os10g41780.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G038487_T01 (Zea mays), 3'ss of exon 5
gtaagaaaagacagctttacatgaactttcatttctgcatgcttccgcatttatttctgaagtcttcagatgaaaatttgccaacagagagaagttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
                               |||   ||| |||      |   || ||| ||| |       | |      ||   |  || | |||  ||  |   | |  | ||| |  || |   ||   |||||||||||||||| || |||||||| |||||||| ||||||||||| ||||||||||||||||||||||||| |||||| |||||||||||||| ||||||||
------------------------------gttttgacattcttat-tgctctcttgtgatgtcgtttatcacaga------aaggcaaggacgatgcataatgaacgtctatgatttataatggt---atgttcttcagGTTGGGAGTACTCTACTGATGGGAAATGTGAAAAAATGCCATCAACAAAGATGCTCAACGTGCGCATCCAGTCATTGCCATGCTTTGAGCAGGAAGGAAT

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171390_T05 (Zea mays), 3'ss of exon 5
gtaagaaaagacagctttacatgaactttcatttctgcatgcttccgcatttatttctgaagtct--tcagatgaa-aatttgccaacagagagaa-gttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
                                                   || ||  |||| |   ||||  ||   |  | |  | | |   |    |||     ||  || | |    | | |     | |||| |||||||||||||||| || || ||||| || || || || ||||||||||||||||||||| |||||||||||| |||  | |||||||||||||| ||||| ||
--------------------------------------------------gtaattaagaaggcaaatcagtcgatcgacctactgaaaaaacaattaatgcacggttaacatataacgcctatata----taataatcttcagGTTGGGAGTACTCGACCGATGGCAAGTGCGAAAAGATGCCATCCACAAAGATGCTCGACGTGCGCATCCAGTCGCTGCCATGCTTTGAGCAGGAAGGGAT

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 5
gtaagaaaagacagctttacatgaactttcatttctgcatgcttccgcatttatttctgaagtcttcagatgaaaatttgccaacagagagaagttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
  |  |||||| |    ||||||||  |          ||      ||| | | || |    | | || || |||| || |          | |||  |||| ||    |  | || |||  ||||            ||| ||||| ||| | |||||||||||||||||||||||||| || ||     |||| || |||   ||   |||||| ||||| |||||   ||| || ||
--atcaaaagatacacatacatgaaaat----------atatcctagcaatgagttatatgttatacacattaaaacttac----------aggtt--gaaaata----tctaattgtttgatgtt------------agGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCGTCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAACAGAGGGGAT

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 5
-----------gtaagaaaagac----agct-----ttacatgaactttcatttctgcatgcttccgcatttatttct-----------gaagtcttcagatgaaaatttgcc--aacagagagaagt-tgcgaaa-gtagtat----ttcagtttttttttgttttca---taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
           || |   | |||    | ||     |||    |  ||    | |   |       ||| | | || |           ||       | |||||||| |  |  | ||  |||   | ||| | | | | ||     | ||| ||     | | |      |     | ||| ||||| ||| | ||||||||||||||||||||||||||||| ||     |||| || |||   ||   |||||| ||||| |||||  |||| |||||
gttagtagtcagtgaatgatgactcttaactccaacttatggaattttctgctccaatacatgatagcaatgagttatatgcactggtagatacacatacatgaaaatatatcctagcaatgagttatatgctatacgcattaaaacatacaggttaaaaatatctaatggttggatgttagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAAAAGAGGGAAT

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 5
----------gtaagaaaagacagctttacatgaactttcatttctgcatgcttccgcat-ttatttctgaagtcttcagatgaaaatttgccaacagagagaagt-tgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
             | || | |    | ||  | | |  | | ||     |  ||    ||  || |   |  ||  |   |    |     || |||||   | ||   |  || | |   | |  |    |||    |   |     ||||| ||||| ||| | ||||||||||||||||||||||||||||| ||      ||| || |||   ||   |||| | |||||||||||  | || |||||
gttagttgtcaccaaaacaaatgattatatcttagcaatgagttaaatgtaattgttgatgctaatgtaggtgtaatttcacattacacaacctacagatttatgtacactgaaattgacatactctaaaatttcaaatggttggatatcagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACAGCTAAATGTGAAAATAAAGTCAGTTCCATGCTTTGAAAAGGAGGGAAT

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G23860.2 (Glycine max), 3'ss of exon 5
----------------gtaagaaaagacagctttaca-tgaacttt---catttctgcatgcttccgcatttatttctgaagtcttcagatgaaaatttgccaacagagagaagttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
                  ||   |  |   | |  || |||| | |   || ||||  || |||    || ||| | | || |   ||    | |   | |  |   |   |   ||  |  |  ||| |  |   |||     |  |  |     ||||| ||||| ||| | ||||||||||||||||||||||||||||| ||  |   ||| || |||   ||   |||| | |||||||||||   ||| |||||
gttagtagtcactgaaacaaatgattatgtcctagcaatgaattatatgcacttcttgatacttgataatgtatgtgt-aatttcacatgacatagcctacagatttatgtacactggaattgacgtactctaaaatttcaaaatggt--tggatatcagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCAACAGCTAAATGTGAAAATAAAGTCAGTTCCATGCTTTGAAAGAGAGGGAAT

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 4
----gtaagaaaagacagctttacatgaactttcatttctgcatgcttccgcatttatttctgaagtcttcagatgaaaatttgccaacagagagaagttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
    ||||||    |  |   ||    ||  || |  | |   ||||         |  |   || ||   |  |   |||     ||   | | |  ||       |  | |   | ||||| |     |  || | ||||||| |||||||| ||||| ||||| ||||| ||||||||||| || |||    |||| || ||    ||    ||||| || || || |||||||| |||||
gttagtaagagggaaaggaaataagcaaaagtttacctgt-tttgctaataagaacagatgacaaatc---aattagtaatgcataaagtaaaaaatatttgtttgctcatgtggaaatttttgtga---tggatgaacttcagGGTGGGAGTACTCAACAGATGGGAAATGCGAGAAAATGCCGTCAACACGATTGCTTAATGTAAAAATAAAATCATTGCCGTGTTTAGAGCAAGAGGGAAT

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|29673392|gb|CB669667.1|CB669667
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|29618942|gb|CB623954.1|CB623954
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|58591367|gb|CF989675.1|CF989675
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|58604859|gb|CK032892.1|CK032892
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|24208889|gb|AU225916.1|AU225916
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|29617556|gb|CB622568.1|CB622568
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|700022|gb|D46313.1|D46313
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|29671152|gb|CB667427.1|CB667427
EST:     GCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: GCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
EST: gi|58611249|gb|CK038961.1|CK038961
EST:     TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATG                         GTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA
genomic: TCTTCATCTTGGCTCAGTTAATGAGGGCAGAATCCAATGCCCTTACCATGgtaagaaaag ... taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagagaagttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
                                          tcataac  putative branch site (score: 2)
                             tttttttttgttttca  CT-rich tract
                     tatttcagtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaagacagctttacatgaactttcatttctgcatgcttccgcatttatttctgaagtcttcagatgaaaatttgccaacagagagaagttgcgaaagtagtatttcagtttttttttgttttcataaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA