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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGGTGACCGTCGACATGCCTTTCACCTCCTACACCTACATTGCCGACCCGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaaccataggatcttcagtgtactgtaaaatgtgccttgcacagtactaacactgacacaaaaaatgtctgaaaatatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g07250.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g07250.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G091822_T01 (Zea mays), 5'ss of exon 1
GACGGTGACCGTCGACATGCCTTTCACCTCCTACACCTACATTGCCGACCCGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaaccataggatcttcagtgtactgtaaaatgtgccttgcacagtactaacactgacacaaaaaatgtctgaaaat-atgcag
||| ||||||||||||||||| ||||| |||||||||||||| || ||||||||||| |||||||||||||| ||||| |||||||||||||||||||||||||| ||  | |    ||     ||| |     | | | |      |||  || | |     |   ||  || ||||| |   || ||
GACAGTGACCGTCGACATGCCGTTCACTTCCTACACCTACATCGCTGACCCGGTGAATGTCGAGCATGTCCTCAAGACTAACTTCACCAATTACCCCAAGgtaaatga--cctgaactcactgatgttc-----agtcttcggaaatcagagctgaaagctgaatcgaatgtgcctgaacaccgtgtag

upper sequence: LOC_Os03g07250.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G69500.1 (Arabidopsis thaliana), 5'ss of exon 1
GACGGTGACCGTCGACATGCCTTTCACCTCCTACACCTACATTGCCGACCCGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaaccataggatcttcagtgtactgtaaaatgtgccttgcacagtactaacactgacacaaaaaatgtctgaaaatatgcag
 || ||    ||    ||||| |||||  | || || ||||| || || ||  | ||||| ||  |||||||||| || |||||| |||||||||||||||| ||| || |      |||| |    | | | |  | |   ||     ||        |          || || |           
AACAGTAGTGGTTCCAATGCCATTCACTACTTATACATACATAGCTGATCCCATCAACGTTGAATATGTCCTGAAAACAAACTTCTCCAATTACCCCAAGgtgaaaaaagc------tctttatatcaatatcatgtatatgttttgttgtgactttgattttttgttgtatatcag-----------
















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|88690459|gb|CI734538.1|CI734538
EST:     CGGTGAACGTNGAGCATGTCCTGAAGAACAACTTCACCAATTACCCCAAG                         GGTGAAGTGTACAGGTCTTA
genomic: CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaac ... aaatatgcagGGTGAAGTGTACAGGTCTTA
EST: gi|88344523|gb|CI677579.1|CI677579
EST:     CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAG                         GGTGAAGTGTACAGGTCTTACATGGATGTGCTGCTCGGTGATGGCATAT
genomic: CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaac ... aaatatgcagGGTGAAGTGTACAGGTCTTACATGGATGTGCTGCTCGGTGATGGCATAT
EST: gi|88665596|gb|CI715752.1|CI715752
EST:     CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAG                         GGTGAAGTGTANAGGT
genomic: CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaac ... aaatatgcagGGTGAAGTGTACAGGT
EST: gi|88442917|gb|CI694329.1|CI694329
EST:     CGGTGAACGTCGAGCATGTCCTGAAGACCAANTTCACCAATTACCCCAAG                         GGTGAAGTGTACAGGTCTTACATGGAT
genomic: CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaac ... aaatatgcagGGTGAAGTGTACAGGTCTTACATGGAT
EST: gi|88668021|gb|CI722760.1|CI722760
EST:     GGTGAACGTCGAGCATGTCCTGAAGAACAACTTCACCAATTNACCC-AAG                         GGTGAAGTGTACAGGTCT
genomic: GGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATT-ACCCCAAGgtaaaagaac ... aaatatgcagGGTGAAGTGTACAGGTCT
EST: gi|88670612|gb|CI724728.1|CI724728
EST:     GGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTNACCC-AAG                         GGTGAAGTGTACAGGTCTTACA
genomic: GGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATT-ACCCCAAGgtaaaagaac ... aaatatgcagGGTGAAGTGTACAGGTCTTACA
EST: gi|88676772|gb|CI730885.1|CI730885
EST:     CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAG                         GGTGAAGTGTACAGGTCTTACATGGATGTGCTGCTCGGTGAT
genomic: CGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaac ... aaatatgcagGGTGAAGTGTACAGGTCTTACATGGATGTGCTGCTCGGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGGTGACCGTCGACATGCCTTTCACCTCCTACACCTACATTGCCGACCCGGTGAACGTCGAGCATGTCCTGAAGACCAACTTCACCAATTACCCCAAGgtaaaagaaccataggatcttcagtgtactgtaaaatgtgccttgcacagtactaacactgacacaaaaaatgtctgaaaatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA