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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaattaagaaatccacaacttgttatattataagcagttacagtctggtcttatcctccctatgtactaatttgtag

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.1 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 7
GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaattaagaaatccacaacttgttatattataagcagttacagtctggt-cttatcctccctatgtactaatttgtag
||||| ||||| || || || |||||||| ||||||||||||||||| |||||  ||||  |     | | ||||      ||||  ||     |     ||   || |  | ||| ||||  | |   |  |        
GTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTGgtgggt--gcttacaaataggatccttggaattcagcagctgatttgcgtttcctgcttttcctggcaaaacaacag-------

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 7
GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaattaagaaatccacaacttgttatattataagcagttacagtctggtcttatcctccctatgtactaatttgtag
||||| ||||| || || || |||||||| ||||||||||||||||| |||||  ||||  |     | | ||||      ||||  ||    | ||||| |  | |   || |  | ||     ||    ||     ||
GTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTGgtgggt--gcttacaaataggatccttggaat----tcagcagctg-atttgcgtttcctgcttttcttggcaaaacaaacag
















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|58602640|gb|CK013168.1|CK013168
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|33381492|gb|CF196835.1|CF196835
EST:     TCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: TCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58686155|gb|CK074842.1|CK074842
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58606572|gb|CK034605.1|CK034605
EST:     ACATACCCATCAACTCAAGCTAGTGGGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: ACATACCCATCAACTCAAGCTA-TGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58687307|gb|CK075994.1|CK075994
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58679602|gb|CK068289.1|CK068289
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58673993|gb|CK062679.1|CK062679
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58602991|gb|CK013519.1|CK013519
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|218486932|gb|FG950343.1|FG950343
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58679239|gb|CK067926.1|CK067926
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|218496430|gb|FG946684.1|FG946684
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58675968|gb|CK064655.1|CK064655
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58682391|gb|CK071078.1|CK071078
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|58679895|gb|CK068582.1|CK068582
EST:     CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG                         GTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
genomic: CACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCT
EST: gi|2317500|gb|C22554.1|C22554
EST:     ATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTC-G                         GTTCTCCCTTG-ACCAGAACATATCGTACATTTGCTCCCGATACTATAGGG
genomic: ATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaat ... taatttgtagG-TCAAGGGAGAACC-GAACATATCGTACATTTGCTCCCGATACTATAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTGgtaagacaattaagaaatccacaacttgttatattataagcagttacagtctggtcttatcctccctatgtactaatttgtag

- - - - - - - - - - -  CAAGCT