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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcacaaaccagttcttttaactccagatttactttctctgtttctcatgtggaagaaagctaatccctaaagctcattcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCTTGTGCTGTGCTGG

Basic information

species Oryza sativa
transcript LOC_Os09g26880.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G130440_T01 (Zea mays), 3'ss of exon 5
gtaggcacaa-accagtt--cttttaactccagatttactttctctgtttctcatgtggaagaaagctaatccctaaagctcattcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCTTGTGCTGTGCTGG
||| ||     | || ||   || | |  ||  || |  |   | ||    |||    | || | ||||||  |||  ||| ||   | |||||||||||||| ||||||||||| |||||||| || ||||| ||||| |||||||||||||| |
gtatgctttttaacaattagtttctcatgccgtatatcatacttttggaaatcagcatgtagcatgctaatggctat-gcttatctgagtagGTGTGGAATCCCCTTGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTG

upper sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaggcacaaaccagttcttttaactccagatttactttctctgtttctcatgtggaagaaagctaatccctaaagctcattcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCTTGTGCTGTGCTGG
    |   |   ||  | | ||   || |  |||  |   ||   |||| | |        | |      ||  | |    | |   || ||||||||||||||||  ||||||||||||||||||| || |||||||| ||||| || || |
----gtgaattgcaagtttgttttgtcaaagttttgtagatccacttcttaggacatgattaacattcggcttgaacattgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG
















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|33676797|gb|CF305036.1|CF305036
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29668655|gb|CB664930.1|CB664930
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29617477|gb|CB622489.1|CB622489
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29668604|gb|CB664879.1|CB664879
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29656047|gb|CB652322.1|CB652322
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|33797257|gb|CF324491.1|CF324491
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29656045|gb|CB652320.1|CB652320
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29668613|gb|CB664888.1|CB664888
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29638871|gb|CB643880.1|CB643880
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|33683878|gb|CF312117.1|CF312117
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGGTGTTATCACAGCATTCAATTTTCC
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTT-GGTGTTATCACAGCATTCAATTTTCC
EST: gi|29665768|gb|CB662043.1|CB662043
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|33681819|gb|CF310058.1|CF310058
EST:     CGCCCGAATCATATGANTGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCC
genomic: CGCCCGAATCATATGA-TGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCC
EST: gi|29673829|gb|CB670104.1|CB670104
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29655872|gb|CB652147.1|CB652147
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29661446|gb|CB657721.1|CB657721
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|33675985|gb|CF304224.1|CF304224
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29674834|gb|CB671109.1|CB671109
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|59930146|gb|AB178688.1|AB178688
EST:     ACGCCCAAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTCCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|58689444|gb|CK078131.1|CK078131
EST:     ACGCCCAAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29673252|gb|CB669527.1|CB669527
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29628521|gb|CB633532.1|CB633532
EST:     ACGCCCAAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29668647|gb|CB664922.1|CB664922
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29677488|gb|CB673763.1|CB673763
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
EST: gi|29668563|gb|CB664838.1|CB664838
EST:     ACGCCCGAATCATATGATGATGGAG                         GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT
genomic: ACGCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCT

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: 57

GCCCGAATCATATGATGATGGAGgtaggcacaa ... attcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCTTGTGCTGTGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttctctgtttctcatgtggaagaaagctaatccctaaagctcattcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCTTGTGCTGTGCTGG
                                  ccctaaa  putative branch site (score: 57)
                                          ctcattc  CT-rich tract
                                             attcaaata  TA-rich tract