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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTCAGACTGTTGCAATGCATGACGCACCTGTCAAGGAGATCGCTTGGATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaatccaatccttgcagcctcggtattcctttttacatggaattcgaattcatatcaaccactctatttactcagatagttattcgctagtaa...

Basic information

species Oryza sativa
transcript LOC_Os08g07960.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 5
AGGCTCAGACTGTTGCAATGCATGACGCACCTGTCAAGGAGATCGCTTGGATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaatccaatccttgcagcctcggtattcctttttacat-ggaattcgaattcatatcaaccactctatttactcagatagttattcgctagtaa
|| ||||||| ||||| |||||||| || |||||||||||| |||| ||||||||||| |||||||||||||| || |||||||||||||||||| ||||||||| ||   |     | |||   ||   ||  |||||||  || |||| | |||| ||||||  | | |  |    || |    |||| | | |     
AGCCTCAGACGGTTGCTATGCATGATGCCCCTGTCAAGGAGGTCGCCTGGATTCCTCAGATGAATCTTCTTGTATCCGGAAGCTGGGATAAGACTTTAAGgtgtgcaagtccagtctcctgctctctaactagacctttttcaattggaagttgaatacatatcc-ctaattcagactcttatgctgttactggttgaatg

upper sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 4
AGGCTCAGACTGTTGCAATGCATGACGCACCTGTCAAGGAGATCGCTTGGATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaatccaatccttgcagcctcggtattcctttttacatggaattcgaattcatatcaaccactctatttactcagatagttattcgctagtaa----------
|  |   ||||||||| |||||||| |||||  |||| ||  | |||||||||||| ||||||| ||| | ||| | ||||||||||| |||||| | | ||   ||    | |    |||| ||||   ||   |  |||   |  || |   ||   ||  ||  |   ||| |     || |  ||| |  || ||           
AACCAATGACTGTTGCCATGCATGATGCACCCATCAAAGAACTTGCTTGGATTCCTGAAATGAACCTTTTAGTCACAGGAAGCTGGGACAAGACTATGAAgt---aatgtgctagcatttgctgcctt--tacagcaatttgtttttaaattatatctttagaaattagaatatat-----gaaaaatatcccgtaatatcaacattata

upper sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 4
AGGCTCAGACTGTTGCAATGCATGACGCACCTGTCAAGGAGATCGCTTGGATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaatccaatccttgcagcctcggtattcctttttacatggaattcgaattcatatcaaccactctatttactcagatagttattcgctagtaa-----
|  |   ||||||||| ||||||||||||||  |||| ||  | |||||||||||| ||||||| ||| | ||| | || |||||||| |||||| | | ||          || |  |||| ||||   ||   |  |||   |  || |   |    ||  ||  |   |||  |   | |||  ||      | ||      
AACCAATGACTGTTGCCATGCATGACGCACCCATCAAAGAAGTTGCTTGGATTCCTGAAATGAACCTTTTAGTCACAGGGAGCTGGGACAAGACTTTGAAgtactgcgctagcatt--ttgctgcctt--tacagcaatttgtttttaaattatacctttagaaattagaatata-agaaaaatatctaaatatcaatattatat

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|33793654|gb|CF322711.1|CF322711
EST:     ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|29615879|gb|CB620891.1|CB620891
EST:     ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|218501857|gb|FG946082.1|FG946082
EST:     ATTCCTCAAATGAATCTTCTTGTCTCTGGAA-CTGGGATAA-ACTCTAAG                         GTA-TGGGACAC-A-GCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|33795033|gb|CF323392.1|CF323392
EST:     ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|29681300|gb|CB677575.1|CB677575
EST:     ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|218492102|gb|FG950663.1|FG950663
EST:     ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACAAGGCAATCAAATCCTGTACATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|58598341|gb|CK008869.1|CK008869
EST:     ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|10794894|gb|AU108860.1|AU108860
EST:     TTCCTCAAATGAATCTTCTTGTCTCTGGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: TTCCTCAAATGAATCTTCTTGTCTCTGG-AAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
EST: gi|25799251|gb|CA755212.1|CA755212
EST:     ATTCCTCANATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAG                         GTATTGGGACACA-GGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA
genomic: ATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGA

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: 70 (upstream exon), 69 (downstream exon)
Score: 26

AGGCTCAGACTGTTGCAATGCATGACGCACCTGTCAAGGAGATCGCTTGGATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaa ... ctatttatagGTATTGGGACACAAGGCAATCAAATCCTGTCCATGTTCAGCAACTTCCTGAGCGCTGTTACGCACTTACAGTGAATTATCCCCTTATGATTGTGGGAACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTCAGACTGTTGCAATGCATGACGCACCTGTCAAGGAGATCGCTTGGATTCCTCAAATGAATCTTCTTGTCTCTGGAAGCTGGGATAAGACTCTAAGgtgtgaaaaatccaatccttgcagcctcggtattcctttttacatggaattcgaattcatatcaaccactctatttactcagatagttattcgctagtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG