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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 14
gtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG
|||||||  |  | ||  | | ||  |  ||    |     |        | || | ||||||   |||  | |  ||               | ||  ||  | ||  ||    ||    |||||  | | ||||| |          | ||||||||| || || |||||  ||||||||||  ||||||| || |||||| | ||||  |||||||||||| | ||||||||||||||||
gtaagtttgaagagcacctctttcggtgttt---gttggata--------tgggctccaccatatggttagctgccta---------------ataggatggatatccctt----tttgcttaagtg-agagaatgtgtg---------tggcagGGTGTGCCGGAGCAGAAGTTGAGGGCACATCTGGGTTCGTTTGGTGTTTCGGGAAGCCTTGCCCTCCAATCTATGTACACTTTATCAG

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 13
gtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatga-agttcaca-gtgtatggatcaccaaacatacagtc-tgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG
                                                         ||   ||| | || ||   ||| ||||  | ||     |  |   |   |||  ||   |    || | | || ||      ||||  |   | | ||||||| || || |||||||| ||  | || ||||| |||||||| ||||| || ||||||||||| || || |||||||| ||||| ||||
-------------------------------------------------------gacaaggtgacaatttacttatgtttggagaaacaggaggaggggggtacctgtgctt--gcaactatgttatta-aattttcctatttgaaattttctgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCGCTGCAGCCAATGTATACTTTGTCAG

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 13
gtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG
                                               ||  | | |   |  | ||   ||| |||| |     | |     ||    ||||   |    | | ||| || ||| | |    | |   ||||    | ||||||||| || || |||||||| ||  | || ||||| |||||||| ||||| || ||||||||||| || || |||||||| ||||| ||||
-----------------------------------------------tgggatgctaggctgtaaa---cacggtgttttttaaaacttgtttagtacctgtgcttgcaattatgtt-atttaaattttccta-ttcgttat---ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------------------------------------------gtaagttcaagcatcatttttatctttcct---ttacatccagcaacaattgctaggttgcacca-tgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG
                                                   | || ||||   | |  |  || |||| |   ||| |     ||    |  |||  |   || | | |  | |||| | || | |   | |||  ||||  |  |  |    | ||  |   |||     |||    | | |||| || | |  |||||| ||||| ||||| || |||||    |||||||||||| | || || || ||||||||||| || || || ||||||||||||||||
gtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaa-gcaaaatgtacataccctcggcttctcaatat--gtct-----taactggtatgttatttgatgtg-gcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 14
gtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG
                                     |  ||    ||| | ||||   |       |   |  | | ||||  | |     |   | | |  ||| ||   || |   |    | || |   ||||   ||  |||  |||||||| || || |||||||| ||  | || || || ||||| || ||||| |||||||||||||| || || || |||||||||||||| |
------------------------------------tctccattttttg-tgggttatcc-------tcttctatttttggaatatc-----ttttgcccgaatgttatc--acatgagt----gaatcactgatgtgaaattggcttcttgcagGGGGTGCCAGAACAGAAGCTCCGAGCTCATTTAGGTTCATTTGGTGTAACAGGAAATCTTGCTCTTCAGCCCATGTACACTTTATCTG

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|427530|gb|D23597.1|D23597
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|27576082|gb|CA998776.1|CA998776
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|22304794|gb|BQ906016.1|BQ906016
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|29623431|gb|CB628442.1|CB628442
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACATTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|3766930|gb|AU031040.1|AU031040
EST:     GCTTGATTTAACAGTGAACCCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTAACCTGNAACAGAAAACTGAGGGCACACTTGGGGGTCTTTCCGGGG
genomic: GCTTGATTTAACAGTGAACCCCC-TTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTA-CCTG-AACAGAAA-CTGAGGGCACACTTGGGT-TCTTTC-GGTG
EST: gi|88841615|gb|CI080871.1|CI080871
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|29676044|gb|CB672319.1|CB672319
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|87013977|gb|CI271368.1|CI271368
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCNT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|27546087|gb|CA764161.2|CA764161
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACATTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|58607561|gb|CK035594.1|CK035594
EST:     TTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACTCT                         GGTGTACCTGAACAGAAACTGAGGGCACATTTGGGTTCTTTCGGTGTTACA
genomic: TTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|29676045|gb|CB672320.1|CB672320
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|86889465|gb|CI317265.1|CI317265
EST:     TTTGTACATGATGAGATGCTACCCT                         GG-G-ACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGGTACA
genomic: TTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|89187105|gb|CI047172.1|CI047172
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|218495876|gb|FG947058.1|FG947058
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACATTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|29664090|gb|CB660365.1|CB660365
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|86903210|gb|CI313573.1|CI313573
EST:     CAGTGAACCCCC-TTTGAACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTT-GGTTCTTTCGGTGTTACA
genomic: CAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|29662748|gb|CB659023.1|CB659023
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|58695639|gb|CK084326.1|CK084326
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACATTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|87016527|gb|CI273737.1|CI273737
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACNCT                         GGTGTACCTGAACAGAAGCTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|29644367|gb|CB649374.1|CB649374
EST:     GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
genomic: GGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA
EST: gi|58696067|gb|CK084754.1|CK084754
EST:     TGAACCCCCTTTTGTACATGATGAGATGCTACCCT                         GGTGTACCTGAACAGAAACTGAGGGCACATTTGGGTTCTTTCGGTGTTACA
genomic: TGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaa ... ctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG
                                           tgctcttt  CT-rich tract
               ttgatctaagtataaa  TA-rich tract