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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgcctagctttgcttgaatatccaagaatagtgtgttgattttattctctctacctattcgatttggactgactggaagtgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGTTATTGTTGTTACTGATGGTGAGCGCATTTTGGGGCTTGGAGATTTGGGT

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 5
splice site 3'
intron type U2

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|58668338|gb|CK057024.1|CK057024
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|319908423|gb|HS977551.1|HS977551
EST:     GGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|58673289|gb|CK061975.1|CK061975
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACCA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|58612495|gb|CK040207.1|CK040207
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|29642462|gb|CB647469.1|CB647469
EST:     GCTTGAAGGACAA                         GGGACAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|218495881|gb|FG947063.1|FG947063
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|58608599|gb|CK036632.1|CK036632
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|29645565|gb|CB650572.1|CB650572
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|2309667|gb|C25822.1|C25822
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGNCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|428653|gb|D24805.1|D24805
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|58667623|gb|CK056309.1|CK056309
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCC
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCC
EST: gi|58595714|gb|CK006242.1|CK006242
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|33796303|gb|CF324019.1|CF324019
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAG
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAG
EST: gi|58674300|gb|CK062986.1|CK062986
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|33793137|gb|CF322449.1|CF322449
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|29668942|gb|CB665217.1|CB665217
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|157651462|gb|EX451096.1|EX451096
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
EST: gi|58672135|gb|CK060821.1|CK060821
EST:     GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAA                         GGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT
genomic: GGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGT

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: 75 (upstream exon), 75 (downstream exon)
Score: 134

TTCTCCCTGTGGTGTATACACCAACAGTAGGTGAGGCCTGCCAGAAGTATGGGAGCATATTTAGACAACCACAGGGTCTCTATGTCAGCTTGAAGGACAAgtatgtttgc ... tgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGTTATTGTTGTTACTGATGGTGAGCGCATTTTGGGGCTTGGAGATTTGGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgattttattctctctacctattcgatttggactgactggaagtgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGTTATTGTTGTTACTGATGGTGAGCGCATTTTGGGGCTTGGAGATTTGGGT
                                gactgac  putative branch site (score: 134)
     ttttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttgcctagctttgcttgaatatccaagaatagtgtgttgattttattctctctacctattcgatttggactgactggaagtgcattctagGGGAAAGGTTCTTGATGTGCTAAGGAACTGGCCAGAGAGAAACATTCAAGTTATTGTTGTTACTGATGGTGAGCGCATTTTGGGGCTTGGAGATTTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT