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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctactttcttttctctctcggttagaacaaggtagagagaacttctaccttatacattcgtatcactgtatgttcttgttggtaaatgttgcctgccagcgtgtattgttttcacgaaagaagagagatgagggaaaaaaaacaatgctgacaattctgttgctctgcgtcttccag

Basic information

species Oryza sativa
transcript LOC_Os07g12530.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12530.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G031780_T02 (Zea mays), 5'ss of exon 8
TGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctactttcttttctctctcggt-tagaacaaggtagagagaacttctaccttatacattcgtat-cactgtatgttcttgttggtaaatgttgcctgccagcgtgtattgttttcacgaaagaagagagatgagggaaaaaaaacaatgctgacaattctgttgctctgcgtcttccag
|||| ||||||| ||||||||||| || |||||||||||||||||||| |||||||||||| |||| ||||| |||||||||||  | ||||||||||||||||| ||||||||| |    ||| || |||||||  |   | ||  || |||||  | |||   |  | ||  | ||  |    |    |||||||   | |                                                                                 
TGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttactttcttctgcaactctgtctagaacagtg---aaaggtctactaccgcaaacaaaaggttacataggataataagctgtaaaaatgttattttc---------------------------------------------------------------------------------

upper sequence: LOC_Os07g12530.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA14G36520.2 (Glycine max), 5'ss of exon 9
TGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctactttcttttctctctcggttagaacaaggtagagagaacttctaccttatacattcgtatcactgtatgttcttgttggtaaatgttgcctgccagcgtgtattgttttcacgaaagaagagagatgagggaaaaaaaacaatgctgacaattctgttgctctgcgtcttccag
 |  ||   |  | |||| | || | |  |  |||| || || ||  | |||||| | || ||||| ||||| |||||||||||| | ||||||||| |||||||||| |||   ||      |   | ||||     | ||| ||||| ||  | | | ||    |   |   || |  |||||      || |   ||  |   ||                                                                          
AGTTGTAGCAACTACAACTGGAACAGCCACAAATGCAACTGCTGTTGCTGCTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctattttagattgaac--caactcgaac---ccaaagacaacttgtatgtca-atataaaaagttcaaaatttaattgttaacttctggtatttg--aatttg--------------------------------------------------------------------------

upper sequence: LOC_Os07g12530.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 5'ss of exon 10
TGAAGTCATAGTTGCAACAGCAAGAACTCCT------GATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctactttcttttctctctcggttagaacaaggtagagagaacttctaccttatacattcgtatcactgtatgttcttgttggtaaatgttgcctgccagcgtgtattgttttcacgaaagaagagagatgagggaaaaaaaacaatgctgacaattctgttgctctgcgtcttccag
       || ||||||||| | |||   ||        |  | || |||||  | |||||||| || ||||| ||||| |||||||||||| | ||||||||| |||| |||  |||||  ||||           ||    | | |  ||| ||| |  |||||||  | | | |   |||| | |  ||||| ||  ||   ||  |     |   || |                                                                  
------TATTGTTGCAACAACCAGAGGCCCATCCACAAACACAACTGCAGTTGCTGCTAATGTAGTTGTTGATGAGAGGCAGATGAATGCACTTTTTCTTGATGTGgtaagc--ctttcaattct----------aaattgtgcaaat-gaatttccaa-ttatacaggcttgtaagcatatggtttcattggttaa-attaggtgtaaagccatgg-gtct------------------------------------------------------------------

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|86501461|gb|CI144094.1|CI144094
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615294|gb|CB620306.1|CB620306
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88224661|gb|CI224510.1|CI224510
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615506|gb|CB620518.1|CB620518
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615267|gb|CB620279.1|CB620279
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88479196|gb|CI416467.1|CI416467
EST:     CATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88560254|gb|CI490900.1|CI490900
EST:     TTTCTTGATCTG                         GTGAGGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCT
genomic: TTTCTTGATCTGgtgagctact ... cgtcttccagGTGA-GGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCT
EST: gi|88491054|gb|CI428326.1|CI428326
EST:     GATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: GATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88541550|gb|CI470827.1|CI470827
EST:     ACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: ACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615259|gb|CB620271.1|CB620271
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615076|gb|CB620089.1|CB620089
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGGGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|86888115|gb|CI300015.1|CI300015
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88465704|gb|CI524654.1|CI524654
EST:     GTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88971605|gb|CI388850.1|CI388850
EST:     GACGAGAGACAGATGAATGCATGGTTTCGTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATGGAAATTTCCTCGCCAATTCGCTCTT
genomic: GACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88487221|gb|CI424492.1|CI424492
EST:     ACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATT-AAATTTCCTCGCGAATTCGCTCTT
genomic: ACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29619071|gb|CB624083.1|CB624083
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88519287|gb|CI446941.1|CI446941
EST:     GAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCCCGAATTCGCTCTT
genomic: GAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88530343|gb|CI458730.1|CI458730
EST:     CTAATGTTGTCNTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615292|gb|CB620304.1|CB620304
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|86254363|gb|CI059090.1|CI059090
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88998076|gb|CI037961.1|CI037961
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|89183900|gb|CI046465.1|CI046465
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88513426|gb|CI440932.1|CI440932
EST:     GATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: GATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615297|gb|CB620309.1|CB620309
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88469764|gb|CI407035.1|CI407035
EST:     CATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCNCGAATTCGCTCTT
genomic: CATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|29615223|gb|CB620236.1|CB620236
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88974078|gb|CI002740.1|CI002740
EST:     TGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: TGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88518906|gb|CI446560.1|CI446560
EST:     GACAGATGAATGCATTGTTTCTGGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCNCGAATTCGCTCTT
genomic: GACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|86493802|gb|CI136435.1|CI136435
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|88508934|gb|CI436440.1|CI436440
EST:     TGTTGTCGTTGACGAGAGACAGATGAATGCATTNTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCNTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: TGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
EST: gi|113931013|gb|DQ884108.1|DQ884108
EST:     CTAATGTTGTCGTTGACGATAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTC
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTC
EST: gi|88964216|gb|CI045409.1|CI045409
EST:     CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTG                         GTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT
genomic: CTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctact ... cgtcttccagGTGAGGGTCAGCGAGTCGTATGGATTGAAATTTCCTCGCGAATTCGCTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctactttcttttctctctcggttagaacaaggtagagagaacttctaccttatacattcgtatcactgtatgttcttgttggtaaatgttgcctgccagcgtgtattgttttcacgaaagaagagagatgagggaaaaaaaacaatgctgacaattctgttgctctgcgtcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG