Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaacatatgtaccctgaaattttccagcaccctcaacatttttttgtttgaactttttttttaaaaaaaaacagaattattcatgctaacttttatggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACT

Basic information

species Oryza sativa
transcript LOC_Os04g46390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 3
------gtaagca-acatatgtaccctgaaattttccagcaccctcaa-catttttttgtttgaactttttttttaaaaaaaaacagaattattcat--gctaactttta--tggttaaca--------gGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACT
      | | ||  || ||  |  | |||  |||          ||||   | |  || |||    | |   |||||| |||     ||||||  ||   || | |   |  |   |||          ||  |||||||||||| | | || |||| ||| ||||||||||| | ||||||||||||||| ||||| || ||  ||||||||||  |    |||||   
gtaagaggatgcttacttaaatttcttgatctttatttattttttcaaatgtgtacttatttcctgtctacctttaaagaaattttcaattatatatttactgattcccaagtatctaattttgtagGTGGTGGTAGCTCAAGAGGAAGAAGGCAGAAACGAGGTGAAGATGTTGTGCATACTTTGAAGGTTTCTTTGGAGGACTTGTATAATGGCACATCAAAGAA---
















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|29637040|gb|CB642049.1|CB642049
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|84117330|gb|CD151097.1|CD151097
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTAC
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTAC
EST: gi|29645124|gb|CB650131.1|CB650131
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33653448|gb|CF276062.1|CF276062
EST:     AATCCATTTGACATATTTGAGCAGTTTTTCGGGGGGTGGTGCCTTTNNNN                         NNNAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
genomic: AATCCATTTGACATATTTGAGCAGTTTTTCGGGGG-TGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGG-AGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
EST: gi|14714017|gb|AU197958.1|AU197958
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|13807441|gb|AU181957.1|AU181957
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGTGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33654740|gb|CF277354.1|CF277354
EST:     AATCCATTTGACATATTTGAGCAGTTTTTCGGGGGGTGGTGCCTTTNNNN                         NNNAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
genomic: AATCCATTTGACATATTTGAGCAGTTTTTCGGGGG-TGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGG-AGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
EST: gi|29678572|gb|CB674847.1|CB674847
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|4715680|gb|AU056796.1|AU056796
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCNAAGAGTACGCAGACAGAGACGTGGTGAAG
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTC-AAGAGTACGCAGACAGAGACGTGGTGAAG
EST: gi|29657304|gb|CB653579.1|CB653579
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33657288|gb|CF279902.1|CF279902
EST:     AATCCATTTGACATATTTGAGCAGTTTTTCGGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: AATCCATTTGACATATTTGAGCAGTTTTTCGGGGG-TGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|218494200|gb|FG946885.1|FG946885
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGT
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGT
EST: gi|58593485|gb|CF991793.1|CF991793
EST:     AAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCACAGAGTACGCAGACAGAGACGTGGTGAA
genomic: AA-TCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCA-AGAGTACGCAGACAGAGACGTGGTGAA
EST: gi|33657059|gb|CF279673.1|CF279673
EST:     AATCCATTTGACATATTTGAGCAGTTTTTCGGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: AATCCATTTGACATATTTGAGCAGTTTTTCGGGGG-TGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29678521|gb|CB674796.1|CB674796
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33694058|gb|CF322297.1|CF322297
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29663531|gb|CB659806.1|CB659806
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|88316124|gb|CI620402.1|CI620402
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAA
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttttttttaaaaaaaaacagaattattcatgctaacttttatggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACT
                                 tgctaac  putative branch site (score: 1)
                                       cttttat  CT-rich tract
     tttttttaaaaaaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaacatatgtaccctgaaattttccagcaccctcaacatttttttgtttgaactttttttttaaaaaaaaacagaattattcatgctaacttttatggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA