Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttccctaatccctacattcttttccccatgtcaattttctcccaagtgagccaacaaaatattaaattagattcttcttttgcattgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g09460.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G092988_T01 (Zea mays), 3'ss of exon 4
gtatgtgttccctaatccctacattcttttccccatgtcaattttctcccaagtgagccaacaaaatattaaattagattcttcttttgcattgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
||| ||| |  || |   ||   |||||  | ||||     | |||| | |  || |      || | || ||     ||    | ||||  |  | |||||| |||||||||||||| | |||||||| |||||||||||||
gtacgtgatttctcacttcttatttcttccctccattatgttattcttctac-tgtgta---gaagtttttaac--agtttgcatcttgctcta-tgcagGATTCCTATAACTGATGGACGTCTCAATACGGGCACTTGGCAG
















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|88211486|gb|CI211126.1|CI211126
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86485004|gb|CI127637.1|CI127637
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88435892|gb|CI514031.1|CI514031
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86528104|gb|CI168310.1|CI168310
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88547724|gb|CI478044.1|CI478044
EST:     ATGACATGCCAGCACATATTAATTCATCAATGTTTGGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCNATATGGGCACTTGGCAG
genomic: ATGACATGCCAGCACATATTAAATCATCAATGTTTGG-TTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88293128|gb|CI512893.1|CI512893
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|9866191|gb|AU101941.1|AU101941
EST:     GATGACATGCCAGCACATATTAAATCATCNATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCNCAATATGGGCNCTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86595369|gb|CI262607.1|CI262607
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86834560|gb|CI344491.1|CI344491
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|40493973|gb|BX901795.1|BX901795
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86414523|gb|CI068926.1|CI068926
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTCGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88259596|gb|CI363889.1|CI363889
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88216643|gb|CI214743.1|CI214743
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88244910|gb|CI242761.1|CI242761
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88979867|gb|CI026167.1|CI026167
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88239487|gb|CI239964.1|CI239964
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88214348|gb|CI214197.1|CI214197
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88526829|gb|CI454918.1|CI454918
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86879801|gb|CI339929.1|CI339929
EST:     ATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: ATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88319148|gb|CI513212.1|CI513212
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86495983|gb|CI138616.1|CI138616
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88243875|gb|CI242997.1|CI242997
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|58664625|gb|CK053311.1|CK053311
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88543260|gb|CI473251.1|CI473251
EST:     ATNACATGCCAGCACATATTAAATCATCAATGTTTGGTTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: ATGACATGCCAGCACATATTAAATCATCAATGTTTGG-TTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86483406|gb|CI126039.1|CI126039
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|86835521|gb|CI347978.1|CI347978
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGCTTGTGCCCTGAC                         GATCCCTATAACTGATTGACATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|88213410|gb|CI213259.1|CI213259
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTTTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
EST: gi|55411794|gb|CV724170.1|CV724170
EST:     GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC                         GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
genomic: GATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG

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: 74 (upstream exon), 61 (downstream exon)
Score: 29

GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttc ... attgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccaagtgagccaacaaaatattaaattagattcttcttttgcattgcttcagGATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG
                                 ttcttcttttgcatt  CT-rich tract
              aacaaaatattaaatt  TA-rich tract