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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattatggcctgaatttttagtcgtttgtatgttgttgtataaactttaaacgaaatttcaaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGT

Basic information

species Oryza sativa
transcript LOC_Os06g43860.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 3
gtaagattatggcctgaatttttagtcgtttgtatgttgttgtataaactttaaacgaaa-tttcaaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGT
||||  ||    | |   ||||| ||  || | | ||  |    ||   | ||| | |||  ||  || || |||||||||||||| || |||||||| ||| ||||||||||| | || |||||||||||||| |||||||| || || || || ||||| || ||||||||||
gtaatgttgaaacat---ttttttgtttttggca-gtaatacactattgtctaagcaaaaactttcaactttcagGGGTACAGAGACAAACTTGTGGATATTCGGGAAGAGATATTGCGGAAGCGAAGAGCTGGGAAACTCCCTGGCGACACTGCTTCTACCTTAAAAGCATGGT
















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|87008402|gb|CI301160.1|CI301160
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29667364|gb|CB663639.1|CB663639
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|58692037|gb|CK080724.1|CK080724
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|58693265|gb|CK081952.1|CK081952
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|58695467|gb|CK084154.1|CK084154
EST:     GATCATTAGTTGAGCGCGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29645298|gb|CB650305.1|CB650305
EST:     AGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: AGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29667393|gb|CB663668.1|CB663668
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29667392|gb|CB663667.1|CB663667
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTACGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29645255|gb|CB650262.1|CB650262
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29645297|gb|CB650304.1|CB650304
EST:     TCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACAGGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: TCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29657258|gb|CB653533.1|CB653533
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29645222|gb|CB650229.1|CB650229
EST:     AAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: AAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29618507|gb|CB623519.1|CB623519
EST:     GATCATTAGTTGAGCGCGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29679811|gb|CB676086.1|CB676086
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|87011013|gb|CI286088.1|CI286088
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29637144|gb|CB642153.1|CB642153
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29663219|gb|CB659494.1|CB659494
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29667365|gb|CB663640.1|CB663640
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29640783|gb|CB645790.1|CB645790
EST:     GAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAAGCTTGTGGACATTAGGGGAAGAGATACTCCGAAAGC
genomic: GAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAG-AAAAGCTTGTGGACATTA-GGGAAGAGATACTCCGAAAGC
EST: gi|58689485|gb|CK078172.1|CK078172
EST:     GATCATTAGTTGAGCGCGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29669194|gb|CB665469.1|CB665469
EST:     GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: GATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
EST: gi|29657867|gb|CB654142.1|CB654142
EST:     ATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAG                         GGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA
genomic: ATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 132

TGGATCAGATGGTATGGGCTTTGGCCCCTTAATGCTGACGGAGGGCGAGAGATCATTAGTTGAGCGTGTACGGCAAGAGCTGAAACATGAGCTTAAACAGgtaagattat ... aaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtcgtttgtatgttgttgtataaactttaaacgaaatttcaaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGT
                                                tttcc  CT-rich tract
                       tataaactttaaacga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattatggcctgaatttttagtcgtttgtatgttgttgtataaactttaaacgaaatttcaaatttccagGGGTACAGAGAAAAGCTTGTGGACATTAGGGAAGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT