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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGAACTTACTACCAGTTTGAGCTGGAACCACCTCATATCTTCATCACTGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactactgttcctatctcaaaactgtatgacattttctttagaactccgaatgctgaataaaagatatggatcgttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g08830.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g08830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G087590_T03 (Zea mays), 5'ss of exon 3
GGAAGAACTTACTACCAGTTTGAGCTGGAACCACCTCATATCTTCATCACTGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactactgttcctatc--tcaaaactgtatgacattttctttagaactccgaatgctg-aataaa-agatatggatcgtt-gcag
|||||||||||||||||||| |||||||| || || ||| | |||||||| || || || ||||| |||||||||||||| |||| |||||||||||| |||||| | | |||||  |    |  || |    |    ||||  |||  |  | ||||  |  |||||| || |  | ||| || ||||
GGAAGAACTTACTACCAGTTCGAGCTGGAGCCGCCCCATGTGTTCATCACCGCCACGGCAGCTGGGAACAGGCTCTACCTCTTCAGTGTAACTGCAAACGgtaaagccattgttcgcagaaatgcaagccaactcttttttttattattatcctgaataatacaataaatagctgggaatcttttgcag

upper sequence: LOC_Os12g08830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA06G12760.1 (Glycine max), 5'ss of exon 4
GGAAGAACTTACTACCAGTTTGAGCTGGAACCACCTCATATCTTCATCACTGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactactgttcctatctcaaaactgtatgacattttctttagaactccgaatgctgaa-taaaagatatggatcgttgcag------------------------------------------
||||||||||||||||||||||||||||| || |||||||| ||||| ||||| || || ||||| ||| |  | ||  ||||   |||||| |  |  |||| | ||| |  ||||   || |||  || | || ||||    |  |    || ||   |  || ||  |||  |  |  ||                                            
GGAAGAACTTACTACCAGTTTGAGCTGGAGCCTCCTCATATTTTCATTACTGCCACCGCAGCTGGCAACCGCTTATATTTGTTTGGTGTAACAGGCAGCGgtatagctatttatcct-cttctaaatagtttcacttttttcacatcatcaagactgaacagctagaaagtatacaaagaagctataagaactaacagaaaataatctaattttttcttaattgcag

upper sequence: LOC_Os12g08830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G42010.1 (Glycine max), 5'ss of exon 4
GGAAGAACTTACTACCAGTTTGAGCTGGAACCACCTCATATCTTCATCACTGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactactgttcctatctcaaaactgtatgacattttctttagaac---tccgaat-gctgaataaaagatatggatcgttgcag---------------------------------------
|||||||||||||||||||||||||| || || || ||||| ||||| ||||| ||||| ||||| ||| |  | ||  ||||    ||||| |  |  |||| | ||| |  ||||   || |||  || | ||  ||||   | | |   || |||  |||  | |  | | |  ||  | |  |                                        
GGAAGAACTTACTACCAGTTTGAGCTAGAGCCTCCCCATATTTTCATTACTGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctatttatcct-cttctaaatagtttcactgtttcacaacatcaagtctgaacagctagaaagtatacaaagaa-gctataagaactaacagaaaataatctaatgttgtcttaattgcag

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|88539844|gb|CI469838.1|CI469838
EST:     TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|88541089|gb|CI469182.1|CI469182
EST:     TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGGCTGAATCA
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATA-GCTGAATCA
EST: gi|27547203|gb|CA765413.2|CA765413
EST:     TGCAACTGCCGCTGGAAACAGGCCCTACATGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|33673774|gb|CF302013.1|CF302013
EST:     TGCAACTGCCGCTGGAAACGGGCTCTACCTGTTCCATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|88533811|gb|CI460479.1|CI460479
EST:     TCCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATNTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|88995772|gb|CI037130.1|CI037130
EST:     TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|88541942|gb|CI471246.1|CI471246
EST:     TGCAACTCCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|88271042|gb|CI386897.1|CI386897
EST:     TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGGCCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|88839416|gb|CI005204.1|CI005204
EST:     TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|88965272|gb|CI009308.1|CI009308
EST:     TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
EST: gi|33666339|gb|CF297306.1|CF297306
EST:     TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATG                         GGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT
genomic: TGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCAT

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: 59 (upstream exon), 74 (downstream exon)
Score: 25

GGAAGAACTTACTACCAGTTTGAGCTGGAACCACCTCATATCTTCATCACTGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactac ... atcgttgcagGGCTACAATGGAAGAGGAATTACAATGACCTGAAGCAAATAGCTGAATCATTTCGTGTTGTCTAGGGTTTAAATAAATTGCTCACGATGTATCTGTTTAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGAACTTACTACCAGTTTGAGCTGGAACCACCTCATATCTTCATCACTGCAACTGCCGCTGGAAACAGGCTCTACCTGTTCAATGTAACTGCAAATGgtaaaactactgttcctatctcaaaactgtatgacattttctttagaactccgaatgctgaataaaagatatggatcgttgcag

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