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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGGAGAGGGTCTCTGCGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgctacctgttccttctaacttgatggaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcag

Basic information

species Oryza sativa
transcript LOC_Os01g16900.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 4
AGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGGAGAGGGTCTCTGCGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgctacc--tgttccttctaacttgatggaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcag
||||||||||||||| ||||||||| ||||||||||||| || ||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||||||||  ||||||  |||| | |     || ||      |     |   || || ||  || || || ||| | | ||  || ||| || |||||  ||
AGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGGAAAGAGTCTCTGCGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggctaccattgtttccttatttttaatcatggatgcctttcgttttatttctttgagaacttatgctttcttgattttttattgtacttgtag

upper sequence: LOC_Os01g16900.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 4
AGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGGAGAGGGTCTCTGCGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgctacc--tgttccttctaacttgatg--gaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcag
||| |||||||| || ||||||||| ||||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||||||||||||||| |||   |||||  |||| | |     || ||   | ||| ||| |||  ||  | ||  |  || || ||||| |  ||| | ||| || |||||  ||
AGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGGAAAGGGTCTCTGCGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtctaccattgtttccttctttttcatcatggatgcatttctt--tttctttctttctgaacttatgtttt-cttgatttttattgtacttgtag

upper sequence: LOC_Os01g16900.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G20790.1 (Glycine max), 5'ss of exon 3
AGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGGAGAGGGTCTCTGCGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgctacctgttccttctaacttgatggaatgtatt-ccttaattcatatcactgggagctgatgttctgtttgttctttgtt-ttactttcag
 ||||||||||| |||||||||||| |  ||||  | |||||||| ||||| |||||||| |||||||| |||   ||||| ||||| |||||||||||||||        |||  | | | | ||      | ||| | |   || || |  |||   ||     |  | ||     || | |||||| ||| ||  ||
TGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAGAGAGGGTTTCTGCCATACACAAAGCCAATATTATGCAAAAGACTGATGGCCTTTTCCTCAAGgtcc-------accaatacttacaaatgcctagaaatttttggtctcaaattttattcatgaattttattatta---atgctttttgttattatttctag

upper sequence: LOC_Os01g16900.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G06590.2 (Glycine max), 5'ss of exon 3
AGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGGAGAGGGTCTCTGCGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgctacctgt---tccttctaacttgatggaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcag
 ||||||||||| |||||||||||| |  ||||  | |||||||| ||||| |||||||| |||||||| |||   ||||| ||||| |||||||||||||||       ||| | |   | | | ||| ||  |||  |  | |  || ||||||     |         | || | |||          ||| ||  ||
TGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAGAGAGGGTTTCTGCCATACACAAAGCCAATATTATGCAAAAGACTGATGGCCTTTTCCTCAAGgtccacc-aatacatataaatgcctataaatttttggtctcaaat--tttattcatgaattttattaacacttttttttttaaaaaa-aaattatttatag

upper sequence: LOC_Os01g16900.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 3
AGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGGAGAGGGTCTCTGCGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgctacctgttccttctaacttgatggaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcag
 |||||||| || ||||||||||||||| ||||  | |||||||| || || |||||||| ||||| ||||||  |||||| ||||| || || || ||||| ||| || |||   | |    |||||| |||     || || || |   ||    |      || | ||   ||||  ||||||| || |      
TGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAGAGAGGGTATCCGCAATACACAAAGCCAACATCATGCAGAAGACTGATGGCCTCTTTCTTAAGgt-tgtctgttacaaatgct---taactttatgttgcataatcatttacctatgcatcct---actaaggtga-gttttctctttgtgttgcag----

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|55410982|gb|CV723358.1|CV723358
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|218503212|gb|FG950056.1|FG950056
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|14571344|gb|BI118712.1|BI118712
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTC-TCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACC
EST: gi|27554384|gb|CA998284.1|CA998284
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCCAG                         TGCTGTCGCGAAGTGGCTGACAAGTACCCTGAA
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAA
EST: gi|27554418|gb|CA998318.1|CA998318
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|41883639|gb|BX928526.1|BX928526
EST:     CGATACACAAGGGCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|58593071|gb|CF991379.1|CF991379
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|55410961|gb|CV723337.1|CV723337
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|29664535|gb|CB660810.1|CB660810
EST:     GCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: GCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|58669476|gb|CK058162.1|CK058162
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|58691994|gb|CK080681.1|CK080681
EST:     GATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGT
genomic: GATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCC-TCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGT
EST: gi|66923182|gb|CX110030.1|CX110030
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAA
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAA
EST: gi|27554444|gb|CA998344.1|CA998344
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|29616640|gb|CB621652.1|CB621652
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|4714232|gb|AU058199.1|AU058199
EST:     CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|29671573|gb|CB667848.1|CB667848
EST:     GGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: GGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
EST: gi|86900281|gb|CI296324.1|CI296324
EST:     CATGAGGAAGACCGATGGTCTTTTCCTCAAG                         TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC
genomic: CATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgc ... ttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGGAGAGGGTCTCTGCGATACACAAGGCCAATATCATGAGGAAGACCGATGGTCTTTTCCTCAAGgtctgtttgctacctgttccttctaacttgatggaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA