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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccaccccacttccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtatgacaagatcttgtgtcaatgttcag

Basic information

species Oryza sativa
transcript LOC_Os06g03970.1
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G082855_T03 (Zea mays), 5'ss of exon 25
GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccaccccactt-ccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtat---gacaagatcttgtgtcaatgttcag-----------------------------------------------------------------
    || ||||| || || || |||||||||||| ||||||| |||||  ||||||| |||| ||||||||| |||||||| || ||| |||| ||  |||| ||  |  || |    ||   ||  ||||   | | |  | | | ||  |   || |   || |      |  |  |  || |||||  ||  | ||  | || |   |    | | || | ||    | |                                                                   
----AACGAGAAGTCCGACGTCTACAGCTTCGGCGTCGTCCTGCTGGAGCTGCTCACGGGGAGGAAGGCCGTGGACAACGAGTCCAACCTGCACCAGCTGGTGAgtgagtccccagatcatcctttgactctgccattt--ttatactggtc---atcacggcctagctagtagatgctgaaggatgatggaaatggtgtctggtttcttggagcggttttttttcgccttgcgcgagtagattatggccgtaacgcatgtctctgctggattaaatcacacgtgtagatactctcgaag

upper sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G082855_T04 (Zea mays), 5'ss of exon 24
GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccaccccactt-ccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtat---gacaagatcttgtgtcaatgttcag-----------------------------------------------------
|||||| ||||| || || || |||||||||||| ||||||| |||||  ||||||| |||| ||||||||| |||||||| || ||| |||| ||  |||| ||  |  || |    ||   ||  ||||   | | |  | | | ||  |   || |   || |      |  |  |  || |||||  ||  | ||  | || |   |    | | || | ||    | |                                                       
GCTCAACGAGAAGTCCGACGTCTACAGCTTCGGCGTCGTCCTGCTGGAGCTGCTCACGGGGAGGAAGGCCGTGGACAACGAGTCCAACCTGCACCAGCTGgtgagtgagtccccagatcatcctttgactctgccattt--ttatactggtc---atcacggcctagctagtagatgctgaaggatgatggaaatggtgtctggtttcttggagcggttttttttcgccttgcgcgagtagattatggccgtaacgcatgtctctgctggattaaatcacacgtgtag

upper sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GLYMA10G38730.1 (Glycine max), 5'ss of exon 26
GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagc-caccccacttccacagttccactccatcctctcat-cacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtatgacaagat-cttgtgtcaatgttcag------------------------------------------
||| ||||| ||||| |||||||| || || || || || || |||||  | || || |||||||||||||| ||||| || || || ||||||||||||||| |   |   |  |  ||       | ||  |  | |  | || ||||    | |  | ||  |||| | ||   |   |    |||   ||| | |  ||  | |    | || | |||   |   | |                                            
GCTGAATGAAAAATCAGATGTGTATAGTTTTGGAATAGTTCTGCTGGAGCTACTTACTGGGAAGAAGGCCGTGGACAATGAGTCCAATTTGCATCAATTGgtatgtgtattactataacatgcactaaatctgtattttggttcatattgattcacaaaaacat-aattgtgga-tatgcatgttttgagtgaatagttttttcattttgtcaaatgcgtgtacaatcatgctaatatacctaaattcttgactcattttttgcatgatttttcag

upper sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 25
lower sequence: AT5G62230.2 (Arabidopsis thaliana), 5'ss of exon 24
GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccaccccacttccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtatgacaagatcttgtgtcaatgttcag
  ||||||||||||| ||| | ||||||||||| || || ||||| ||  | ||||| |||||||| || || || |||||| | |||||||||||| |||||    |  | |    |||  |   |    ||  |||    || ||    | | ||| |     || |     | ||  ||                                                 
AATCAATGAGAAATCCGATATATACAGCTTCGGTATTGTTCTTCTTGAGCTTCTCACTGGGAAGAAAGCAGTGGATAACGAAGCTAACTTGCATCAACTGgtatatgaatcaagaatcactat---agattatgatctttgaacctta-aaagagttaacgttttttttttttatgttgcag-------------------------------------------------

upper sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 25
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 5'ss of exon 25
GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccaccccacttccacagttc-cactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtatgacaagatcttgtgtcaatgttcag----------------------------------------------------------------------
||||||||| ||||||||||| || || || ||||| |||||||||||  |||| ||||||||||| || || ||||| ||||| || ||||||||| ||||| |  || | |   |||  |||    ||  ||  | |  |  ||       |  || | |    |     ||  |  ||   ||  |   | ||   | |   ||| |||||  || |   |   || ||                                                                      
GCTCAATGAAAAATCTGATGTTTATAGTTTTGGCATTGTCCTTCTGGAGCTGCTGACAGGGAAGAAAGCTGTAGACAATGAATCAAATTTGCATCAACTGgtatgttactctaaccccaatgtttgtgctatatatttttgttccaaaacttgatttttttat--gtcaggcaaactggcttttat--tttgaagggcaagtgccatg-caagaatttattaaataatttagattttcaaacatctcttgggttatgttacgaaaatggttaagtaattgattttttaactttgctgctcag

upper sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 25
lower sequence: PP1S20_166V6.1 (Physcomitrella patens), 5'ss of exon 4
GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccaccccacttccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtatgacaagatcttgtgtcaatgttcag
  | ||||| ||||| || || ||||||||||||||||| ||||||||| | ||  |    ||||| || |||||  |||||  |||  | |   | | ||||   || | || |  ||   |||  |      |  |  |||  | ||  ||    ||     | |  ||  |||     | |        ||| |  ||||||                          
CTTGAATGAAAAATCAGACGTCTACAGCTTCGGCATCGTTCTTCTGGAAATTCTGGCCAACAAGAAAGCAGTCGATGACGAAGTGAATCTCCTAGACTGGgta---caactcaatcacagccttcttcatgtggcagtattcagctcgttgaactgaattgttgaatgaaggtctt-----gtactgattgttggtttgtttgtag-------------------------

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|86479702|gb|CI122335.1|CI122335
EST:     TGCTCACAGGGAAGAAGCCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|58668197|gb|CK056883.1|CK056883
EST:     CGACAACGAATCGAACTTGCATCAAGTTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGA
genomic: CGACAACGAATCGAACTTGCATCAA-TTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGA
EST: gi|163926182|gb|EG711834.1|EG711834
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|38482930|gb|CF966732.1|CF966732
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACGGCACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|2317603|gb|C22657.1|C22657
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATANTCTCCAAAGCTGATG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATG
EST: gi|38479012|gb|CF963145.1|CF963145
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAGAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|66923246|gb|CX110094.1|CX110094
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|2317602|gb|C22656.1|C22656
EST:     AAGAA-GCCCTCG-CAACGAATCGAACTTGCATCAATTG                         -TACTCTCCAAAGCTGATG-CCACACAGTCATGGAGGCATTGGCCTCGGAG
genomic: AAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|38477005|gb|CF961138.1|CF961138
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|58661800|gb|CK050480.1|CK050480
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGC
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGC
EST: gi|38477623|gb|CF961756.1|CF961756
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGT
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGT

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: 63 (upstream exon), 57 (downstream exon)
Score: 9

GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAGGTGTCAGTGACGTGCACGGACATGGGACTGGTCAGGAAGGCCTTCCAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccaccccacttccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtatgacaagatcttgtgtcaatgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG