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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagcacacatacttgtctacggcttttgcccatatcatttccatctgtctggctgattattttaatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG

Basic information

species Oryza sativa
transcript LOC_Os01g73970.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
-------gtatgcagcacacatacttgtctacggcttttgcccatatca----tttccatctgtctggctgatt--attttaatct--------ttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG
       |||   || | | ||    ||  |      || |  | || |    ||   | |  | ||  | | |   ||||||| |        |||||||| |||||||| ||||| |||||  ||||||| ||||||||||| ||||||||  ||||||||||||||||||||
gtaaatagtaaatagtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
-----------------gtatgcagcacacatacttgtctacgg-cttttgcccatatcatttccatctgtctggct---gattattttaatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG
                 |  | |        |||||   ||    ||| | |  |  |   ||   | | | | |||     ||   ||  | ||||||||| |||||||| ||||| |||||  ||||||| ||||||||||| ||||||||  ||||||||||||||||||||
gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 12
gtatgcagcacacatacttgtct-acggcttttgcccatatcatttccatctgtctggc--tgattattt-------taatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG-------------------------
||| |  |        |    ||  |     ||    | |  || | |   || |||    |||  ||||       |    |||||||||||| |||||||| || ||||| || ||||| ||||||||  ||||| ||||| | ||||| ||||| |  ||                          
gtaagttgtttttgccccccccttgcttaccttaataacacaatattctcttgactgatgatgaaaatttgtgtgttttgcttttgcagCCTGCTCATGAGAAGATTGGTGTTGTGGATTCGCAATGGATAATACATAAAGTGATACCTTCACTTGGAAGTCAAGGAAAGTCAGAGAATGGGAAAGCTC

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------------------gtatgcagcacacatacttgtctacggcttttgcccatatcatttccatctgtctggctgattattttaatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG
                                      |  | |||     ||  | || | |   | | |   |    | ||||||||| ||  || |    |  |  |||||||||||| |||||||| || ||||| || ||||| || |||||| | ||||||||| ||||||| ||||| |  |||
gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctc-atgaactctccttgttaagtctccatctgtatg--tggtctcctcca--tttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 12
---------------------gtatgcagcacacatacttgtctacggctt-ttgcccatatcatttccatctgtc-tggctgattattttaatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG
                      |  ||     || |  || ||  |    |  |  | || | |  || |    |  | | |  |   |||  ||||| |||||||||||||||||||||||||| |||||||| || |||||| | ||| |||| || ||||||||||||| ||| 
cagatattttatatttttcttttgggctaacaacctttttatcagcaatctactttctatttgacatcaactcataattgttactggattt--tctttacagCCTGCACATGAGAAAATCGGTGTGGTTGATTCACAGTGGATTATTCATAAAGTAGTACCTTCTCTTGGGAGCCAA

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|86841951|gb|CI338360.1|CI338360
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|86424012|gb|CI062773.1|CI062773
EST:     AGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: AGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|88470908|gb|CI408179.1|CI408179
EST:     GTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: GTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|58595145|gb|CF993453.1|CF993453
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|86536269|gb|CI176475.1|CI176475
EST:     ACTTGGTTCATGGATGGGGTCTTGATGTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|12404721|gb|AU166322.1|AU166322
EST:     TGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: TGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|86893421|gb|CI313341.1|CI313341
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|88522872|gb|CI450665.1|CI450665
EST:     TGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: TGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|1854181|gb|AA231809.1|AA231809
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|29663566|gb|CB659841.1|CB659841
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|88489023|gb|CI426294.1|CI426294
EST:     TCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: TCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|88902346|gb|CI374954.1|CI374954
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|3760914|gb|C98168.1|C98168
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|29641985|gb|CB646992.1|CB646992
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|86526488|gb|CI166694.1|CI166694
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|5803529|gb|AI978499.1|AI978499
EST:     GGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGNNNGTACATCAA
genomic: GGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|86888761|gb|CI307819.1|CI307819
EST:     ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: ACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
EST: gi|88663212|gb|CI479204.1|CI479204
EST:     GATTTCGCTCTCAGAAGATGTGTAGAT                         CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA
genomic: GATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAA

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), 63 (downstream exon)
Score: 43

AATGACTTGGTTCATGGATGGGGTCTTGATTTCGCTCTCAGAAGATGTGTAGATgtatgcagca ... atctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggcttttgcccatatcatttccatctgtctggctgattattttaatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG
                                        ttttaat  putative branch site (score: 43)
                                              tctttgc  CT-rich tract
                                  tgattattttaatctt  TA-rich tract