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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGCGTGCTCCAGGAGATCAAGCGCCGCCGCCGCTACGAGAGCAAGAAGGACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacacctcacctccccccctttgtttgatgcatcgatattgtctatgaaatgatgtaatcctttttgtgaattgtgaattcttgaaatcgatata...

Basic information

species Oryza sativa
transcript LOC_Os02g09590.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G076263_T01 (Zea mays), 5'ss of exon 1
CCGGCGTGCTCCAGGAGATCAAGCGCCGCCGCCGCTACGAGAGCAAGAAGGACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacacctcacctccccccctttgtttgatgcatcgatattgtctatgaaatgatgtaatcctttttgtgaattgtgaattcttgaaatcgatata-----
|||||||||| ||||||||||||||||| ||  | || |||||||||| |||||||   ||||||||||| ||||||||||| |||||||||||||||||||   | ||   |  | | ||      ||| | ||   |  |||||  || || |  | | || || ||  |     ||||    ||     |     |      
CCGGCGTGCTGCAGGAGATCAAGCGCCGTCGGAGGTATGAGAGCAAGACGGACGAGAAGAAGCGCAAGGCGCGCGAGGCCGGGCGCCGCAACCGCCGCAGgtatgagcatggctgcgctccg-----gttcgctgtccctctattggataggagagtacggaacccgttcaggatgatgtgcgcactgcccctgtgctttcttgt

upper sequence: LOC_Os02g09590.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G145962_T01 (Zea mays), 5'ss of exon 1
CCGGCGTGCTCCAGGAGATCAAGCGCCGCCGCCGCTACGAGAGCAAGAAGGACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacacctcacctccccccctttgtttgatgcatcgatattgtctatgaaatgatgtaatcctttttgtgaattgtgaattct---tgaaatcgatata--
|||||||||| ||||||||||||||||||||  | |||||||||||||  ||||||   ||||||||||| ||||||||||| ||||||||||| |||||||  |    | || ||||   |    |    ||   |||| | |  ||      | ||||    | | |||| | |     || | |   | |  ||  || |  
CCGGCGTGCTGCAGGAGATCAAGCGCCGCCGGAGGTACGAGAGCAAGACAGACGAGAAGAAGCGCAAGGCGCGCGAGGCCGGACGCCGCAACCGTCGCAGgt--atgtgcttcccctcatgctgcata---gaccaatcgttctactcctgttcaggatgcctacttgtttgcggaagccaaactgtctatcagttctctaaaag
















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|86887055|gb|CI325870.1|CI325870
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
EST: gi|58593922|gb|CF992230.1|CF992230
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
EST: gi|38475849|gb|CF959982.1|CF959982
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATGCGGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
EST: gi|58587159|gb|CF985467.1|CF985467
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAG
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAG
EST: gi|29622535|gb|CB627546.1|CB627546
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
EST: gi|38475019|gb|CF959152.1|CF959152
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTACCCAGAAGACGATGCTGATTCAGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
EST: gi|38475977|gb|CF960110.1|CF960110
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
EST: gi|38471940|gb|CF956071.1|CF956071
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
EST: gi|38474858|gb|CF958991.1|CF958991
EST:     GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAG                         GCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC
genomic: GACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGC

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: 71 (upstream exon), 41 (downstream exon)
Score: 6

CCGGCGTGCTCCAGGAGATCAAGCGCCGCCGCCGCTACGAGAGCAAGAAGGACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacac ... tgttgtgcagGCGTATGATGGAGGAGCCTAGGTTCCCAGAAGACGATGCTGATTCAGAGGCCGCGAGGAGGGCTCGTGACGATGAAAAGGATAACTGGGAGATTGACGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGCGTGCTCCAGGAGATCAAGCGCCGCCGCCGCTACGAGAGCAAGAAGGACGAGCGCAAGCGCAAGGCCCGCGAGGCCGGCCGCCGCAACCGCCGCAGgtgaaaacacctcacctccccccctttgtttgatgcatcgatattgtctatgaaatgatgtaatcctttttgtgaattgtgaattcttgaaatcgatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc