Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaattttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA

Basic information

species Oryza sativa
transcript LOC_Os01g55350.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 8
-------------cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaattttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
             |||  || || ||||||    ||  || |   | |||  |  |  ||||| |  |    ||  | |||   || ||| |||    |   |||      |||| ||||| ||| |||| ||||| || ||||| ||||| ||| | || |||||||||||||| |||||||| |||||||||||||||||||| |||||||
aagaaacatttctctttcctttggagtcacaactatttatcttgcaatttatt--tccttattttctttccttgctttaatg--ctgaatattg----taaactgc-----agGCTACACCTGAGCTGGAGTATGGAAGAATGAACATTGGCAGTCGTCCGTCAAAACGAAAGCCAAGTGGAGGAATTGAATCACTTCGTGCAATCCCTTGGA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 9
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaattttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
 ||   |||    |    |   | || |  | |   | || || |   | ||| |  | |  ||  ||  | |    ||      | |  ||      ||||||| || |||||||| ||||| || ||||| ||||| ||| | |||||||| |||||||| |||||||| ||||||||||| ||||| ||||||||||
tttttttctcctttggagtcatttaactaatgaaaatacttatcacattgctatttctttccattgattctgttttattcatgaatattatgcactgcagGCAACTCCTGAGTTGGAGTATGGAAGAATGAACATTGGCAGTCGTCCATCAAAGCGAAAGCCAAGTGGAGGAATTGAATCACTACGTGCTATTCCTTGGA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 8
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaattttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
 ||  | ||    |    |   | || |  | |   | || ||||   |   | |  | |   |  ||  | |    |||     | |  ||      ||||||| || |||||||| ||||| || ||||| ||||| ||| | |||||||| |||||||| |||||||| ||||||||||| ||||| ||||||||||
tttttccctcctttggagtcatttaactaatgaaaatacttatgacactgtaatttctttcctttgattctgtttcatttatgaatattgtgcactgcagGCAACTCCTGAGTTGGAGTATGGAAGAATGAACATTGGCAGTCGTCCATCAAAGCGAAAGCCAAGTGGAGGAATTGAATCACTACGTGCTATTCCTTGGA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 8
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaatt-ttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
  ||  |     ||| |       |||||  |  |   ||  | |||    |||       | ||||| ||  ||||   ||     ||  | |||  ||||| |||||||||||||| ||||| |||||||||||||||||| | ||| ||||  |||  |||||||||||||||||| |||| |||||||| |||||||
-gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 9
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctg---tataaataatctcaatt-ttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
    | ||  ||     |  |   |  |  ||   |    ||    | |  || |    ||   | ||||| ||  ||||   ||     ||  | |||  ||||| ||||| |||||||| ||||| |||||||| ||||||||| | ||| ||||  ||||||||||||||||||||||| |||| |||||||| |||||||
----agtccttaaaaggcccccagatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 8
cttcact---ctgtagtcacct--tcataaatttgttattttgcta-atgattattctaatggtctgtataaataatctcaattttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
 || | |   |||    |||||  | | |||   | |   ||| |  ||   ||  || |   |     | || |||| | ||    |  | ||| ||  |   |||| ||||| |||||||||||||| |||||||| ||||||||| | ||  ||||  | | ||| |||||||| |||||  |||| || || || |||||||
-tttatttaactgattccacctagtgagaaaaaggcttggttgttgtataggtaaactgacatttgaatttaacaatcactat----caaccttg-tgaaatgcagGCCACACCTGAGTTGGAATATGGAAGGATGAACATTGGAAGTCGACCGGCAAAGAGGAGGCCAAGTGGAGGTATTGAGACACTGCGCGCCATACCTTGGA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 8
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaattttgcttct-ttgctgtcaaat--agGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
  |||   | |  |  | || | ||||   ||  |  ||     |||  ||     |   | |  |||  |     | ||   ||| || || | ||||  ||||||| ||||||||||| |||||  ||||||| ||||||||| | ||||||||||||||||| ||||| |||||||| ||||| || ||||| || ||||
--tcataatttgcttgcatttacaaata-attcctgagccctgcatttctcactgtgaaggcaataatggtgatggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA

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|88972798|gb|CI717524.1|CI717524
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTG
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTG
EST: gi|66932214|gb|CX119062.1|CX119062
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAAGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88955081|gb|CI721744.1|CI721744
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCAT
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCAT
EST: gi|88670955|gb|CI725071.1|CI725071
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88904996|gb|CI712295.1|CI712295
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATNGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88904883|gb|CI712182.1|CI712182
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATCGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88671110|gb|CI725226.1|CI725226
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATCTCCGCCTT                         GCCACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88667085|gb|CI719221.1|CI719221
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88904826|gb|CI712125.1|CI712125
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCAT
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCAT
EST: gi|88972712|gb|CI717438.1|CI717438
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGT
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGT
EST: gi|88675137|gb|CI729250.1|CI729250
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATCTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGC
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGC
EST: gi|88984087|gb|CI723647.1|CI723647
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGT
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGT
EST: gi|88670962|gb|CI725078.1|CI725078
EST:     ACCGGTCCATTGTCTCCCAAGAGGCACGATTNGTTGAATATTTCCGCCTT                         GCAACACCCGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88670921|gb|CI725037.1|CI725037
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88687965|gb|CI731541.1|CI731541
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88904468|gb|CI711776.1|CI711776
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCCA-C
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCC-ATC
EST: gi|88594427|gb|CI714385.1|CI714385
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAAT
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAAT
EST: gi|88672471|gb|CI726587.1|CI726587
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCA
EST: gi|88905576|gb|CI712875.1|CI712875
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTCGGAATATGGTAGGATGAATATNGGAAGT
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGT
EST: gi|88666010|gb|CI716166.1|CI716166
EST:     ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTT                         GCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGG
genomic: ACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGG

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: 41 (upstream exon), 10 (downstream exon)
Score: 1

AGAATGGCGTGCTTTGATGGATGAAATGGCCGCTGTTGCTACAAAAGAATACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattc ... tgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattctaatggtctgtataaataatctcaattttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
   ttctaat  putative branch site (score: 1)
                               ttttgcttctttgct  putative PPT
              tgtataaataatctca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaattttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - caccttc
- - - - - - - - - - - - - - - - - - -gctaatg