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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGTATTCAACTTTTGTTTTCCAGAAGCCTGACCCAGATGCAATGCCACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctgcatttagcaggtgttgatatttactatcacattttactgatatttttttgttaactgtgagtgaaatatcag

Basic information

species Oryza sativa
transcript LOC_Os02g54000.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54000.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G171410_T04 (Zea mays), 5'ss of exon 11
GCTTGTATTCAACTTTTGTTTTCCAGAAGCCTGACCCAGATGCAATGCCACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctgcatttagcaggtgttgatatttactatcacattttactgatatttttttgttaactgtgagtgaaatatcag-------------
||||||||||| | ||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||| |||| ||||||||| || | ||| ||||||||||| |||   | |     |    |    |   | |    ||||| |     |||  |   || |||   ||   || ||              
GCTTGTATTCAGCATTTGTGTTCCAGAAGCCTGATCCAGAGGCAATACCACCGATTGTAACTCCCGACTTGCCTGATCCTGATAAAGGTCACGAAGAGgtctggtctatttcttctgtgctcagtagctagttgtatgtttttattttctgtttcattggaaatgttgttggtctaacactttgactgaacag

upper sequence: LOC_Os02g54000.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G171410_T01 (Zea mays), 5'ss of exon 10
GCTTGTATTCAACTTTTGTTTTCCAGAAGCCTGACCCAGATGCAATGCCACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctg---------ctctgcatttagcaggtgttgatat---ttactatcacattttactg-atatttttttgtta----actgtgagtgaaatatcag
||||||||||| | ||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||| |||| ||||||||| || | ||| |||||||||||          ||||   | || || |  |  |||   ||  | |    ||| | || | || || ||| |     ||| ||| ||||  | |||
GCTTGTATTCAGCATTTGTGTTCCAGAAGCCTGATCCAGAGGCAATACCACCGATTGTAACTCCCGACTTGCCTGATCCTGATAAAGGTCACGAAGAGgtctggtctatttcttctgtgctcagtagctagttgtatgtttttattttctgtttcattggaaatgttgttggtctaacactttgactgaa-cagcag
















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|88228725|gb|CI228205.1|CI228205
EST:     CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAG                         GAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
genomic: CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
EST: gi|6431606|gb|AU081258.1|AU081258
EST:     CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAG                         GAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
genomic: CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
EST: gi|88228791|gb|CI228271.1|CI228271
EST:     CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAG                         GAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
genomic: CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
EST: gi|89197193|gb|CI051923.1|CI051923
EST:     CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAG                         GAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
genomic: CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
EST: gi|117219854|gb|CT852296.1|CT852296
EST:     ATCAAGAAGAG                         GAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
genomic: ATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
EST: gi|88271658|gb|CI387711.1|CI387711
EST:     CACCAATTGTAACACCCGAATTTCATGATCCTGAGAATGATCAAGAAGAG                         GAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
genomic: CACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT
EST: gi|6431607|gb|AU081259.1|AU081259
EST:     ACCAATTGTAACCCCCCGAAATGCATGATCCTGAGAATGATCAAGAAGAG                         GAATGCCTCTGGACGCAGCAGNCATCAATGGCCGATGGAAGGGTCTCACGT
genomic: ACCAATTGTAA-CACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGT

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: 64 (upstream exon), 41 (downstream exon)
Score: 9

GCTTGTATTCAACTTTTGTTTTCCAGAAGCCTGACCCAGATGCAATGCCACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctg ... gaaatatcagGAATGGCTCTGGACGCAGCAGGCATCAATGGACGATGGAAGGGTCTCACGTACTGATATACTTCCTCCTGCGGATAATGAGAAAGGCATCCTTGGTCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGTATTCAACTTTTGTTTTCCAGAAGCCTGACCCAGATGCAATGCCACCAATTGTAACACCCGAATTGCATGATCCTGAGAATGATCAAGAAGAGgtctgctctgcatttagcaggtgttgatatttactatcacattttactgatatttttttgttaactgtgagtgaaatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG