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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGACATCATCGAATCTGCCGTCAGAGACGCCGTTTCCAAGGAGTCTCGCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctcacacaactcacccttttaagttcagttttccttctcgttttctagtccgacctttgaagtagatgtttcaatttcgaaattcgctagtcgc...

Basic information

species Oryza sativa
transcript LOC_Os04g55740.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55740.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G443885_T01 (Zea mays), 5'ss of exon 1
GCTCGACATCATCGAATCTGCCGTCAGAGACGCCGTTTCCAAGGAGTCTCGCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctcacacaactcaccctt---ttaagttcagttttccttctcgttttctagtccgacctttgaagtagatgtttcaatttcgaaattcgctagtcgc--------------------------------------------------------------------------------------------------------
           |||| || || || ||||  ||||| ||||||||||| |||||||| || || || || ||||||||||||||||||||||||||||||||||||  ||     | ||||  |   ||   |||||  ||||   |   ||| |     ||  ||      |  || | | ||     |  | ||   |  |                                                                                                        
-----------TCGAGTCCGCAGTGAGAGCTGCCGTCTCCAAGGAGTCCCGCATGGGGGCCTCCCTCCTCCGCCTCCATTTCCACGACTGCTTTGTCAATGCAAGTGCCATgtgccacacctctaaatttccttcagccttccacttttgtttttcccatgaagttacgttaaactgatgccatgcatgagctagccgttgactgaactgacgggcttcggttagatcttctactgttttgggcggagtgtttagaatcttgcttattaggcatagcacatcatatgttggttcagacattcagtag

upper sequence: LOC_Os04g55740.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G40000.1 (Glycine max), 5'ss of exon 1
GCTCGACATCATCGAATCTGCCGTCAGAGACGCCGTTTCCAAGGAGTCTCGCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtct-cacacaactcacccttttaagttcagttttccttctcgttttctagtccgacctttgaagtagatgtttcaatttcgaaattcgctagtcgc------
 |||   |||||| || | || || |  |  || ||| | || |||   ||||||||||| ||  |||| || || |||||||| |||||||||||||||||| || | |    |||  | |||    || |     || ||    ||    || ||  |    |    ||  || || |||||||||      ||           
TCTCTCTATCATCAAAACGGCGGTGATTGGTGCGGTTGCGAAAGAGCACCGCATGGGAGCCTCCTTGCTCCGTCTTCATTTCCATGACTGCTTTGTCAATgcacgttttcttttaacatatcct----agcttcacctttctcactgtcaattaatctcatgcata---tatgtgattaaatttcgaacaataatatatattggcat

upper sequence: LOC_Os04g55740.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv08s0058g00980.t01 (Vitis vinifera), 5'ss of exon 1
GCTCGACATCATCGAATCTGCCGTCAGAGACGCCGTTTCCAAGGAGTCTCGCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctcacacaactcacccttttaagttcagttttccttctcgttt--tctagtccgacctttgaagtagatgtttcaatttcgaaattcgctagtcgc----
 ||    || ||| ||||||| || |     || ||    |  ||  |||||||||| || || ||||| || || |||||||||||||||||||| ||||||||||    || |||  | | | ||  | || ||||| |   | |||  |||   ||    | | |  |   ||  |   |||  |  ||  |     ||    
CCTTTCAATAATCAAATCTGCAGTGAACTCTGCAGTGAAGAGTGAAGCTCGCATGGGGGCGTCCCTGCTCCGTCTTCATTTCCACGACTGCTTTGTTAATgcaagtc----accacttcctcatatatctcca-ttttcatgagcctttaatcttaaccattttataatattc-tgcatggctttatacttttacctcatgcttgt

upper sequence: LOC_Os04g55740.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv06s0004g07740.t01 (Vitis vinifera), 5'ss of exon 1
GCTCGACATCATCGAATCTGCCGTCAGAGACGCCGTTTCCAAGGAGTCTCGCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctcacacaactcacccttttaagttcagttttccttctcgttttctagtccgacctttgaagtagatgtttcaatttcgaaattcgctagtcgc--
                                                    ||||| |||||  |||| || |||||||||||||| |||||||| ||||||||| |       |||  |  ||  | |  | ||||  |  | ||  |   |    | | |   |    ||  ||   ||||    |    | |      
----------------------------------------------------ATGGGGGCTTCTTTGCTTCGTCTCCATTTCCACGATTGCTTTGTTAATgcaagttttctct--ctcttctcttccattataatttttttctttgtccttgtgctatatcctcttacattataattttttttccttgtcattttggtatat

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|88741177|gb|CI764685.1|CI764685
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
EST: gi|88353904|gb|CI634695.1|CI634695
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGGTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
EST: gi|88763968|gb|CI773384.1|CI773384
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
EST: gi|88733297|gb|CI756474.1|CI756474
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTG
EST: gi|88763072|gb|CI772628.1|CI772628
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
EST: gi|88762724|gb|CI772280.1|CI772280
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
EST: gi|88761965|gb|CI771521.1|CI771521
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
EST: gi|88315333|gb|CI613602.1|CI613602
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGGTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGGCGAG
EST: gi|88740550|gb|CI764058.1|CI764058
EST:     GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAAT                         GGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGG
genomic: GCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctca ... gcgcgtgcagGGGTGTGACGGGTCAGTGCTGCTCGACGACACGGCGGCCATCACCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGACATCATCGAATCTGCCGTCAGAGACGCCGTTTCCAAGGAGTCTCGCATGGGAGCTTCGCTGCTGCGCCTCCATTTCCACGACTGCTTTGTCAATgcaagtctcacacaactcacccttttaagttcagttttccttctcgttttctagtccgacctttgaagtagatgtttcaatttcgaaattcgctagtcgc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaccc