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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGGGGGCGGCTGCCGAACGGAAGCGGAAGCGCGCCGCCGCCGCCAAGACCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaacctacctggggttcgggtttgggttggaaagcgctgcctctcgctcgcttctgctgctgctgctactgctgctaattctgctcccatgatt...

Basic information

species Oryza sativa
transcript LOC_Os03g58340.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58340.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G004290_T01 (Zea mays), 5'ss of exon 1
CGCGGGGGCGGCTGCCGAACGGAAGCGGAAGCG---CGCCGCCGCCGCCAAGACCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaacctacctggggttcgg--gtttgggttggaaagcgctgcctctcgctcgcttctgctgctgctgctactgctgctaattctgctcccatgatt
    |  || | |||||| || |||||||||||   |||||||||||||||||||   ||||| ||||||||||||||||||||||||||| | ||||||||||||  |      |||||||||  |   |  || | | | |||   |  || | ||| |  |     ||||    |  |   | |  || |||    |||| |
---TGCCGCTGTTGCCGACCGCAAGCGGAAGCGGACCGCCGCCGCCGCCAAGACCACCTCCCTTAAGAACCAGATCCGCTCCACCGAGCGCTTCCTCCGCAAGgtacttaccgacacctggggtctgctcggctgagctcggaaggtttagctgttgcttg--tggagcgctgtgtgttttctgggtctttttgcaatgatgaat

upper sequence: LOC_Os03g58340.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G32310.1 (Glycine max), 5'ss of exon 1
-CGCGGGGGCGGCTGCCGAACGGAAGCGGAAGCGCGCCGCCGCCGCCAAGA-CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaacctacctggggttcgggtttgggttgga--aagcgctgcctctcgctcgcttctgctgctgctgctactgctgctaattctgctcccatgatt
 ||  |   |  || || | |     ||| | |||   |  | |   |    ||||||||||||| |||||||| || |||   |||||| ||||||||||||||||    |  |||             |    |      |    |   |  |  ||  |||| |     ||| || ||| |                    
GCGTAGATCCAACT-CCAAGCCTCT-CGGCATCGCCAAGAAGTCCAAACCCTCCGTTTCCCTCAAAAACCAGATTCGATCCCTTGAGCGCATGCTCCGCAAGgtaacaaccctaaccctaaccctaaccctaaccttatttgattattcgtttccattcatttctccga--actggtattgcag--------------------

upper sequence: LOC_Os03g58340.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA20G35300.1 (Glycine max), 5'ss of exon 1
---CGCGGGGGCGGCTGCCGAACGGAAGCGGAAGCGCGCCGCCGCCGCCAAGACCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaa--cctacctggggttcgggtttgggttggaaagcgctgcctctcgctcgcttctgctgctgctgctactgctgctaattctgctcccatgatt
   |  |     ||    ||    |||||  |||| |    ||    ||    ||||||||||||| |||||||| || |||   |||||| ||||||||||||||||   |  |||| |      ||   |     ||||       |   |  |  ||  |||| |     ||| ||  || |                    
CTCCAAGCCTCTGGGCATCGCCAAGAAGCCCAAGCCCAAGCCCAAGCCCT---CCGTTTCCCTCAAAAACCAGATTCGATCCCTTGAGCGCATGCTCCGCAAGgtaaccctaaccctagccctaactcta-tccctattggct--tattcgtttccattcatttctccga--actggtatagcag--------------------

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|88727569|gb|CI751224.1|CI751224
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|88395426|gb|CI612948.1|CI612948
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|88349431|gb|CI653710.1|CI653710
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|88324146|gb|CI563757.1|CI563757
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|66918908|gb|CX105756.1|CX105756
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|88377677|gb|CI605512.1|CI605512
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|88739193|gb|CI762701.1|CI762701
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|86596668|gb|CI286581.1|CI286581
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
EST: gi|88576591|gb|CI670736.1|CI670736
EST:     CCGTTTCCCTCAAGAACCAGATCCGCTCC-CCGAGCGCCTGCTCCGCAAG                         GACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG
genomic: CCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 32 (upstream exon), 55 (downstream exon)
Score: 15

CGCGGGGGCGGCTGCCGAACGGAAGCGGAAGCGCGCCGCCGCCGCCAAGACCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaac ... atttggtcagGACCTTCCTAATGACATTAGGGTAGCTCAAGAGAAGAAACTGGAAGAATTGAAGCGGCAACAAGAGCTTCAGAATCAACTGGCTATTCAACGAACAGTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGGGGGCGGCTGCCGAACGGAAGCGGAAGCGCGCCGCCGCCGCCAAGACCGTTTCCCTCAAGAACCAGATCCGCTCCACCGAGCGCCTGCTCCGCAAGgtaacttaacctacctggggttcgggtttgggttggaaagcgctgcctctcgctcgcttctgctgctgctgctactgctgctaattctgctcccatgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctccc