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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatgaagatttactcttgctgacttaaatatcatcatctttgctcaactcagcaataactgctttattctcag

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G081322_T01 (Zea mays), 5'ss of exon 19
TGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatg------atatgaagat-ttactcttgctgacttaa-atatcatcatctttgctcaactc--agcaataactgctttattctcag
 |||||||||||| | |||||||||||  | || || ||||||||||||||||||||||||||  | ||||| || ||||| |||||||| |||||||||||| |       | | ||  | |||  ||| |||  ||    |   ||||   | |  ||||||  |||||  | |||||   || |||
CGAAGACATGATGATACTTGATACACACTGTGAGGTTTTTGTTTGGATGGGTCAGTGTGTGGAGACAAAAGAAAAACAGAAAGCATTTGACATTGGCCAGgtaggtaccaagtgttaaagtgttaacctttctgtttttttgttggatcactatcgtccaactcctagcaacgattgcttccctcccag

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G359566_T01 (Zea mays), 5'ss of exon 3
TGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatgaagatttactcttgctgacttaaatatcatcatctttgctcaactc--agcaataactgctttattctcag
 |||||||||||| | |||||||||||    || || ||||| |||||||||||||| |||||  | ||||| || ||||| |||||||| |||||||||||| | ||  |||  |||  ||| |||  ||   |   ||||   |    ||| ||  |||||  | |||||   || |||
CGAAGACATGATGATACTTGATACACACTCTGAGGTTTTTGTCTGGATGGGTCAGTGCGTGGAGACAAAAGAAAAACAGAAAGCATTTGACATTGGCCAGgta-ggtaccaagtgttaacctttctgtttttggttggatcactatcttccaaatcctagcaacgattgcttccctcccag

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA03G29280.1 (Glycine max), 5'ss of exon 17
TGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatgaagatttactcttgctgacttaaatatcatcatctttgctcaactcagcaataactgc--tttattctcag
 || || ||  || | ||||| ||||| |  ||||| ||||| ||||| ||||||||||||||  | ||||| ||||| || || |||||||||| |||||||  | |||   |   | |  |   | ||| | |  | | || |    | |  | |   | ||  |   |||  ||||||
AGAGGATATCCTGATCCTTGACACACACGCAGAAGTGTTTGTATGGATTGGTCAGTGTGTGGACCCAAAAGAAAAGCAAAATGCTTTTGAAATTGCCCAGgta-aacatgctcaacaaat--tagagccttcatttcccttatttccttttacttgatgtacaatagaaattttctctcag

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA19G32010.1 (Glycine max), 5'ss of exon 18
TGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgta----tgatatgaagattta--ctcttgctgacttaaatatcatcatctttgctcaactcagcaataactgc--tttattctcag
 ||||| ||  || | ||||| || ||    ||||| ||||||||||| ||||||||||||||  | ||||| ||||| || || |||||||||| |||||||    || |    | |||    |  |  ||  | | | |  | |   |||     |  | |   ||||  |   |||  ||||||
AGAAGATATCCTGATCCTTGACACGCACACAGAAGTGTTTGTTTGGATTGGTCAGTGTGTGGACCCAAAAGAAAAGCAAAAAGCTTTTGAAATTGCCCAGgtaaacatgctcaacaaattagagccttcacttcccttatttccttttacttgatgtacttgatgtataatagaaattttctctcag

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|88694289|gb|CI738327.1|CI738327
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|58596217|gb|CK006745.1|CK006745
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|25798468|gb|CA754429.1|CA754429
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|396941448|gb|HO188657.1|HO188657
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|88718464|gb|CI741974.1|CI741974
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|33674859|gb|CF303098.1|CF303098
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|58674368|gb|CK063054.1|CK063054
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|58610643|gb|CK038355.1|CK038355
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|58672994|gb|CK061680.1|CK061680
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
EST: gi|58652765|gb|CK041445.1|CK041445
EST:     GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAG                         AAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT
genomic: GTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatg ... ttattctcagAAATATGCAGAACATGCGGCGGCCTTCGAATCTCTTTCTCCTGATGTGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTGTGGATGCTAAAGAGAAGCAGAAGGCATTTGAAATTGGCCAGgtatgatatgaagatttactcttgctgacttaaatatcatcatctttgctcaactcagcaataactgctttattctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC