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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 14
GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcag
||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||||  ||||| || |||||||  |  | ||  | | ||  |  ||    |     |        | || | ||||||   |||  | |  ||      |    |   | | ||  ||| |  || |  |      |  || |   |                       
GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCGgtaagtttgaagagcacctctttcggtgttt---gttggata--------tgggctccaccatatggttagctgccta------ataggatggata-tccctttttgcttaagtgagagaatgtgtgtggcag----------------------

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 5'ss of exon 14
GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaagcatcatt---tttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcag
|||||||| ||||| |||| |||||||||||||||||| || ||  || |    || ||||||||||| |||||| | |||||||| || ||||| |   | | |   |  || || | ||||   |  |  || ||| ||   |       |    ||    |||| ||      ||| |||   | |                                                        
GTTCGCATTGCTGTGTTCAGTCAACACCATGTTGATGGCCTAGACCTATCTTCAAATCCCCTTTTGTATATGATGCGCTGCTACCCAgtgagttctaatgttactaaatacattttccttttattccttgagacgatttctttttcctttttttttcttgtgtgtgtgtgtgcttgcaagcatt--gcc--------------------------------------------------------
















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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCTgtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG