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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttattattatggtatcaattgtgggtcatgacgagcaattctttctacacatattcag

Basic information

species Oryza sativa
transcript LOC_Os02g08544.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G433591_T02 (Zea mays), 5'ss of exon 5
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttatta--ttatggtatcaattgtgggtcat-gacgagcaattctttctacacatattcag
||||||| | ||||| || || ||||| || |||||||| ||||| |||||| |||| ||||||||||||||||||||||| |||||||| |||||||||||||||| ||||       ||  |   |  | |  |||  || || |||||  |  || |||| || |||||| |||||    ||   | |||
AGAGATCATGCGCAAACGCAGGGCTGGGAAGCTTCCTGGAGATACCGCATCTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgacacc---gcgtcaacttaattccctcgttagcttctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccag

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 4
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttatta--ttatggtatcaattgtgggtcatgac-gagcaattctttctacacatattcag
||||||  | |||||||| |||||||| ||||||||||| |||||||||||| | || ||||||||||||||||||||||| ||||||||||||||||||||| ||| ||| |      ||| |   |  | |  | |  || || |||||  |  || ||||  | || | | |||||    |   || |||
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgacactacggcgacatata-attccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccag

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA06G06890.2 (Glycine max), 5'ss of exon 4
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgta------cgtggcaccaacattccatttccgtaactttattatta------tggtatcaatt--gtgggtcatgacgagcaattctttctacacatattcag
 || ||  | || ||| |  ||||||| |||||||||||||| ||  | ||| | || ||||||||||||||| | ||||| |||||||| || || || |||      |  | |   |  ||    |||  | || |   ||   |      | | |  ||||   ||  | |  || |  |  || || |||| || |    
GGAAATTTTACGTAAGAGACGAGCTGGGAAACTTCCTGGTGACACGACCTCTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTATCCTACGgtaagaactcaagactttactatgtttttttaggaaatccctttcaaacaaatttgaacgaatttaatgaataacaacaaagatgtccttgtacatattt----

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G06810.1 (Glycine max), 5'ss of exon 5
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttattattatggtatcaattgtgggtcatgacgagcaattctttctacacatattcag-------------
 || ||  | |||||| |  ||||||| |||||||||||||| ||  | ||| | || ||||||||||||||| | ||||| |||||||| ||||| || |||   |   |||| | |  | | |  |   ||| || | |    | |  ||       |    || | | | |    |     |   |              
GGAAATTTTACGCAAGAGACGAGCTGGGAAACTTCCTGGTGACACGACCTCTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCCACAgtaa--gaacccaagactttactac-attttttttttctcagtaaacccttttcaaacaaatttgaacgaatttaaagaatagcaacaaagatgaccttgtac

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G32980.2 (Glycine max), 5'ss of exon 4
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttattattatggtatcaattgtgggtcatgacgagcaattctttctacacatattcag----------
 || ||  | |||||| | ||||| || |||||||||||||| ||  | ||| | || ||||||||||||||| | ||||| |||||||| ||||| || ||| ||   |  || |     |    ||     |   || ||| | |        | |  | |  |  | ||  ||||  ||  |   ||          
GGAAATTTTGCGCAAGAGAAGAGCAGGGAAACTTCCTGGTGACACAACTTCTGTTCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCTACCgtaagtttgataaataagaattcaatgtgtacattacatcatgcttttggaaaaagcttttaagaattatttgattcttaactaacgaagtccttgtaag

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA14G13750.2 (Glycine max), 5'ss of exon 4
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttattattatggtatcaattgtgggtcatgacgagcaattctttctacacatattcag-------------
 || ||| | |||||| | |||||||| |||||||||||||| ||  | ||| | || ||||||||||||||| | ||||| |||||||| ||||| || ||| ||   |  || |    |  ||  ||| |  ||| |||    |    || ||||  |   |    ||   | |   | ||  ||  |             
GGAAATCTTGCGCAAGAGAAGAGCTGGGAAACTTCCTGGTGACACAACTTCTGTTCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCTACCgtaagtttgataaataag--aactcaataagtacatttttacatcaagctttttgggaaaaagcttttaaacatataggc-caagtttggattaatatttagt

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|29640689|gb|CB645698.1|CB645698
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|29640688|gb|CB645697.1|CB645697
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|29663726|gb|CB660001.1|CB660001
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|29661445|gb|CB657720.1|CB657720
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|3760309|gb|C97565.1|C97565
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|88302049|gb|CI667895.1|CI667895
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAG
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAG
EST: gi|29670827|gb|CB667102.1|CB667102
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttattattatggtatcaattgtgggtcatgacgagcaattctttctacacatattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA