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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatggatgatggtggttttggctggcag

Basic information

species Oryza sativa
transcript LOC_Os10g42940.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G011518_T03 (Zea mays), 5'ss of exon 1
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAG--AAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatg-gatgatggtggtt--ttggctggcag-------------
  |    || | ||||||||  |   |||  ||| | |  ||| |||||||||||||||||| ||||| || || ||||||||||||||||||||||||||||||| |    ||  | |  || ||| |  |    |||   |    | | |   ||||  ||  ||||    || |  | |     | |             
--GCGGCCTCCCAGATCCGGTTGGATCGAGGGGCAAGGTCAAGAGATGGGGCAGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgt-ctccttccttcctgtttcccctcgctcccttcccatctcgacaggatactgcaatgaatcgggctcctcgataaaccgatccgttcacaaa

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 1
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatggatgatggtggttttggc-tggcag--------------
 |      |||| |||  |       ||       |   ||| ||||| || || || || |||||||||||| ||||||||||||| |  |||||||||||  |        |||  |  |  | | | |  |      |    || |      ||||  | | ||  |  |  |    |   |               
ATAATCAGTTCTCGATTTGATTTGATCGGAACAGAACAGAGGCATGGGTCAAGCTTTTCGGAAGCTCTTCGACACCTTCTTCGGCAATACCGAGATGCGGgtctcttccttccttctccattccttttttttattattattctttttcttttaatatcaacggtcataataatgataatataataattctaagaagaaga

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA12G02110.1 (Glycine max), 5'ss of exon 1
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtacc--ccaagcttttccactcttgtctgtc--tcgtctcag-attgggttttggacggatcatggatga-tggtggt-----tttggctggcag----
 |    | |||| |||  |      |         | ||||| ||||| || || || || |||||||||||| |||||||||||||||  |||||||||||  |  ||   ||| |||| || |   |  |    |||  |  | ||    |   |    || | || || | |  ||     ||||  |   |     
TTTTGTGATTCTCGATTTGATTTGGATCGCACAGAACGAAGGCATGGGTCAAGCTTTTCGGAAGCTCTTCGACACCTTCTTCGGCAACACCGAGATGCGGgtctcttccttccttctccattccttaatagcaacagtcataataatgataatataataattcttagaagaatagatgtcattttttgcttaataacgct

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 5'ss of exon 1
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactct---tgtctg--tctcgtctcagattgggttttggacgga------------tcatggatgatggtggttttggctggcag
 |  ||       |    ||      |  |    |    || |||||| ||  | || |||||||| |||||  |||||||||||||| |||||||| |||||| |      | ||||   |   | | ||  |   || |  ||| |  |  ||||||||             ||| | | || ||  |  | |||  |  
GTAAAATTCGTCTGTGGGGGTTTAAGCTTTTTTGGGGTGAGAGATGGGTCAAACTTTTCGCAAGCTTTTCGATACCTTCTTCGGCAACCAGGAGATGAGGgtactctccttctctccatcttctgtatttgatttctgtatttgatcgtttactggacggaatcgcgtgttacccatcgttaatcgttatactcgctttc--

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatggatgatggtggttttggctggcag------------------
    ||   |  |||       |    ||      ||| ||| ||||| || ||||| ||||||||||||||  ||||||||||||||   |||||| ||||||||     |||  |  |||| |   |  | |  |   |||  || ||         |  |||    |  |||||  | |                     
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccct--tttttctctatctttttctttacatacccatttgtattatgtgttt-ctgtatatgggtttctttttgtttcgtttcaattcatttctttttat

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 1
-----CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatggatgatggtggttttggctggcag------------------
      ||   ||| ||    |  |   ||  | | |     || |  |||||| |  | |||||||||||||| ||| || |||||||||||||||||||||||||||    |  | | ||   ||    | || ||       ||||  | ||   ||   ||   || | || || |||| | |  |                  
CGTGCTTGAGTGCTACTG---CTCGTTCCTGGGGTAGCTC--GAGGCTATGGGGAACACTTTCCGCAAGCTCTTTGACTCCATCTTCGGCAACAAGGAGATGCGGgtacgttcatatctgccgaactc-cgtatcgcggtgattgttggcgtctg--tggtgaatacttgtttgttgtcttggttcgtgggttgttgctgttcctctc

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 5'ss of exon 1
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgt------ctgtctcgtctcagattgggttt-tggacggatcatggatgatggtggttttg-gctggcag-------
                                           ||||||||| | ||||| |||||||||||  || | ||||||||||||||||||||||| | || | ||   | ||| || |       ||| ||    ||| ||   ||| | |    | ||    || | | ||||||| |    |||       
-------------------------------------------ATGGGGCAGACTTTCCGGAAGCTCTTCGATTCCATTTTCGGCAACAAGGAGATGCGGgtgcgcccatctccgctacttttctacccaattgtgtctgtgcagtttttctttctcgtttcaccaactttggtagaggttttgcggatccagtggaagt

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 5'ss of exon 1
CTGGAAGCTTCTAGATCCGGCCGCTACGATC-GGCGAA---GAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgt-ctgtctcgtctcagattgg--gttttggacggat---catggatgatggtggttttggctggcag---------
     ||     ||    |   |||| | |  || ||    ||||  |||||| |  |||||||||||||||| ||  |  ||||||||||||||||||||||||||| ||||  |    || | | || |    |  | |||   ||   ||||  ||   |    | |   |  | || |||| | ||   ||         
----CAGTCCAGAGTAGGGATTGCTAGGTTAAGGTGAGCTTGAAGCTATGGGGAATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGGgtacgccaatatccgtcattatcgtgcaactttatgtcatcgtgactgtttgcgataaacttgcgtctctatttgttgtttcgcctaataggtttgcctt

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|88764833|gb|CI773951.1|CI773951
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88430649|gb|CI596763.1|CI596763
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88738429|gb|CI761937.1|CI761937
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|29641419|gb|CB646426.1|CB646426
EST:     GCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: GCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88765119|gb|CI774225.1|CI774225
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|66919127|gb|CX105975.1|CX105975
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGAGCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88405972|gb|CI591367.1|CI591367
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGATAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88415237|gb|CI584060.1|CI584060
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88761917|gb|CI771473.1|CI771473
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|218479927|gb|FG968408.1|FG968408
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88735828|gb|CI757403.1|CI757403
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88307304|gb|CI641942.1|CI641942
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|33811779|gb|CF331776.1|CF331776
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|33795688|gb|CF323714.1|CF323714
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|218479871|gb|FG966995.1|FG966995
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAGGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88743152|gb|CI766660.1|CI766660
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88574643|gb|CI666412.1|CI666412
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
EST: gi|88426529|gb|CI579358.1|CI579358
EST:     AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAAAAAGGAGATGCGG                         GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG
genomic: AGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaag ... tggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatggatgatggtggttttggctggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG