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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGACGCCGGCAGCACCGGCACACGGGTGCACGTCTTCAGGTTCGACAACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacattaatctaatctactacctccgtttcaggttataagactttttagcattgtccatattcatatatatgctaatgaatctagacacacatat...

Basic information

species Oryza sativa
transcript LOC_Os12g02980.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g02980.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G431714_T01 (Zea mays), 5'ss of exon 1
ATTGGACGCCGGCAGCACCGGCACACGGGTGCACGTCTTCAGGTTCGACAACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccaca--------ttaatctaatctactacctccgtttcaggttata-agactttttagcattgtccatattcatatatatgctaatgaatctagacacacatat------------------------------
 || |||||||||||||| || || ||| ||||||||||||||||||||||| |  |||||||  ||  | ||||| ||  ||||||| ||||||| |||||    | |        |  || ||  |  |  | |||| | ||    ||  | |   | | |       |   ||    ||  |||||  |  | || |    | |                                
CTTCGACGCCGGCAGCACGGGGACCCGGATGCACGTCTTCAGGTTCGACAACCACATGGACCTGGTCGGGATCGGCCACGGCATCGAGTTCTTCGCCAAGgtgtatatagatatagatagatatatacagcctcatccgatccatcgcattcacagcatatggagacaaacccgtttccctacgtgctacgggttgtacaatgtcgtcgtcggcgttgtttggtggcgcatgcatgcag

upper sequence: LOC_Os12g02980.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G006762_T01 (Zea mays), 5'ss of exon 1
ATTGGACGCCGGCAGCACCGGCACACGGGTGCACGTCTTCAGGTTCGACAACAAGCTGGACCTCCTCAAGGTCGGCGACAAC---ATCGAGCTCTTCGCTAAGgtaaccacattaatctaatctactacctccgtttcaggttataagactttttagcattgtccatattcatatatatgctaatgaatctagacacacatat
    |||||||||||||| || || || || |||||||||||||||||||  ||||| || |||||| || |||||||| ||   |||||| | ||||| |||||    | ||  || |  | |     |  ||        ||||  |   | ||    | |    ||| |     |  ||  ||  | | |   ||     
---CGACGCCGGCAGCACAGGGACCCGTGTACACGTCTTCAGGTTCGACAGGAAGCTCGAGCTCCTCGAGATCGGCGACGACGGCATCGAGGTGTTCGCCAAGgt----atatatatgtggtttgacggcatcgaggtgttctatat-atagtctatatatatatggattaaggagcaaacttttgtttgttgctgcag----
















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|88718255|gb|CI741344.1|CI741344
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|163928679|gb|EG710928.1|EG710928
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|88693195|gb|CI736770.1|CI736770
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|88301463|gb|CI597156.1|CI597156
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|58594578|gb|CF992886.1|CF992886
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|29657813|gb|CB654088.1|CB654088
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|88431154|gb|CI574325.1|CI574325
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATC-TGGGCTGAGCTCCTACGCTGGACGTC-TCAGGATGGCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|29660868|gb|CB657143.1|CB657143
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|58668446|gb|CK057132.1|CK057132
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|29619276|gb|CB624288.1|CB624288
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|88399133|gb|CI603800.1|CI603800
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|66924334|gb|CX111182.1|CX111182
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|88391706|gb|CI600895.1|CI600895
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|88717473|gb|CI740983.1|CI740983
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|58601501|gb|CK012029.1|CK012029
EST:     ACAAGCTGGAGCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|29616330|gb|CB621342.1|CB621342
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|4715162|gb|AU056279.1|AU056279
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|29616586|gb|CB621598.1|CB621598
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
EST: gi|88720452|gb|CI743751.1|CI743751
EST:     ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAG                         GTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC
genomic: ACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacat ... gttgttgtagGTGGATCCTGGGCTGAGCTCCTACGCTGGACGTCCTCAGGATGCCGCAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGACGCCGGCAGCACCGGCACACGGGTGCACGTCTTCAGGTTCGACAACAAGCTGGACCTCCTCAAGGTCGGCGACAACATCGAGCTCTTCGCTAAGgtaaccacattaatctaatctactacctccgtttcaggttataagactttttagcattgtccatattcatatatatgctaatgaatctagacacacatat

- - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC