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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcag

Basic information

species Oryza sativa
transcript LOC_Os03g15780.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G161337_T02 (Zea mays), 5'ss of exon 7
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcag
|||||||||| |||||||||||||||| ||  |||||||||||||||||||||| || || || |||||||| || |||||||||||||||||||| ||||| ||| ||  |||||  | ||        |||  |    |  |||  |    | || ||  |||    |  | | ||||| | ||   | |||  |        
GAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAACAGTGTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtatttctttttccctattagaactccataatatagtacattgcat---tctgatataaatacaatg-ctatttttcctttgggaaatttggatccatac-

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA18G03270.1 (Glycine max), 5'ss of exon 7
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcag
  | ||||||| || |   ||   |    | || || |||||||| |||||||| || ||| | ||| | || ||||||||| | |||||||||||||||||||||  | |   | ||| ||   | |   ||  |   |||  |||      | |   |||  | |   | |||    |      ||||  || | | |   | 
TGAAGAAGATGCAAGGTTTGAAGCAATATTGCTGAGAGATGAAAAGCAGTGTGCAGAGCATGTCATGTTGGTTGATTTGGGACGCAATGATGTTGGAAAGgtttgt--tataaatattcaata--taatggatactcctatttgtttttttcctgttcaaggtgtcttgaagcaatagcttggtcaattatattgttcatttaa-

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA18G03260.1 (Glycine max), 5'ss of exon 8
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttg-tgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcag-
  | ||||||| || |  |||   |   || || || |||||||| |||||||| || ||| | ||| | || ||||||||| | |||||||||||||||||||| | |   |   |||  |||| | | || |  ||   |||  |||    |  |||   |||      || | |||     || || | | | || ||      
TGAAGAAGATGCAAGGTTAGAAGCAATACTGCTGAGAGATGAAAAGCAGTGTGCAGAGCATGTCATGTTGGTTGATTTGGGACGCAATGATGTTGGAAAGgtttgctatagatacattttaatggat-attcctatttat-ttatcttgttcaaggtgtcttgaag----caatagcttgctcaattat-attgtttatttaaagaa

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G29690.1 (Arabidopsis thaliana), 5'ss of exon 8
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttctt-----ttttttcgatggctgagtcatggttgcattaatttgac----agattt-gttaggaatgtgttaacaacttttcttatgattactttctacttggcag
 || ||||||  |||||  ||  || ||||  |||| ||||||||||| || || ||||||||||||||||| |||||||||||||| |||||||| ||||||  |    ||     |  ||||  |  | |  || |     | |   || ||     ||||   |||   | |  ||   | |  ||  |    |||  | |  |||  |   
CAAAGAAGATCTAATGCTGGAAAAAGAGCTCTTAAGCGATGAAAAACAATGCGCAGAACATATTATGCTTGTTGATTTGGGAAGGAACGATGTTGGCAAGgttcatcactttaccactgctttcactttcagtctcttaccctcttcttttagaagctaagatgcagttcttactcggtagtctaacttgttggatattcttgtaaactcag---

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G55870.1 (Arabidopsis thaliana), 5'ss of exon 8
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttcttttt---------tttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaac--aacttttcttatgattactttctacttggcag------------------------------------------------------------------------
  |||| ||| |||||   ||| |    ||  |||  ||||||||||||||||| ||||| || ||||| || || |||||  | |||||||||||||||||| || |  || |          | | | |     | || |||||  |  |||     | |    | |   ||   |||||  |  |  |  ||||   |  || |   |  ||                                                                         
CGAGGAGGATCAAATGTTGGAGGAGGCACTTTTAAAAGATGAAAAACAGTGTGCAGAACACATCATGCTCGTTGACTTGGGTCGCAATGATGTTGGAAAGgttagtctgtttctcaggatcaaatctggtttatatattcttggtttaagcaatgatgaaaaacgatcaatgat-cattaacttacgtacttctatgccaatcttttctcttacaaagaatatttcaaatttgaacatatagtattgtctaatatctcattggctctctctgggccttatgaaaccag

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv13s0067g00400.t01 (Vitis vinifera), 5'ss of exon 8
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttcttttttttcgatggctgagtcatg-gttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcag
  | |||||||| |||   ||    || || |||| |||||||||||| ||||| ||||| |||||||| || ||| ||||  | ||| ||||||||||||||| | ||       |||  |     |  |||   ||   |    || | || |||      |  |  |   |   |  | ||     |   |||||        
CCATGAAGATGAGATGTTGGAAGGGCAACTGCTAAATGATGAAAAACAATGTGCAGAACACATTATGCTGGTTGATCTGGGGCGAAATAATGTTGGAAAGgtttctcttaaccaacttcctttatgaaaacatctattatgtagtgtttaaagctttaagcccatagcttgctcgtttggtgtttctgctgaattctatc------

upper sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 5'ss of exon 8
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtt---tgtgttcttttttttcgatggctgagtcatggtt--gcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcag
 || ||||||   |||   ||  | ||||| |  | ||||||||| |||||||||||||| |||||| | || |||||||||||||||||||||||||||||    ||    ||  | | |   |   | | | ||  ||  | || | | |     |||   ||    |  |||   ||   ||  |   | | |  |  |        
TAAAGAAGATATCATGTTGGAAAACCAGCTTCGGAATGATGAAAAGCAGTGTGCTGAACACATTATGTTGGTTGATTTGGGAAGGAATGATGTTGGAAAGgtgaagtgcaccctaatgtcttatttattca-taataattctgaatgattctagagtattctataattttaggttggaaatagtttct-caactccccttaa--------

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|29616044|gb|CB621056.1|CB621056
EST:     TGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTT-GANAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACG
genomic: TGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGA-AAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACG
EST: gi|29662736|gb|CB659011.1|CB659011
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGGATGATG-TGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29646546|gb|CB651553.1|CB651553
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29662735|gb|CB659010.1|CB659010
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29628879|gb|CB633890.1|CB633890
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
EST: gi|29614551|gb|CB619564.1|CB619564
EST:     GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAG                         GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC
genomic: GTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttc ... tacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAACAGTGTGCTGAACATATTATGCTTGTAGATTTGGGAAGGAATGATGTTGGAAAGgtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA