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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtaagatacatcacacaacttctcaaactctttcactactttggagtaaattcctgtatcataacttaacttaccaagtatttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT

Basic information

species Oryza sativa
transcript LOC_Os10g35960.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------------gtgcgtaagatacatcacacaacttctc---------aaactctttcactactttggagtaaattcctgtat-cataacttaacttaccaagtatttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT
                                                                                     |   | | |  |   |  |   || |          |||   | |   |||||   | ||||| | ||  | |||| ||||       |||  ||| | ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||| ||||| |||||||||||||| |||||||||||
gtgcgtgagatacattaaacctaatttctgaaatgtttttatcatggcaccttttttacaacattttcataaccattgctttgattaaatgaaagtctgaatgctgtttgtttatggaaaaaaaagatgtatttacttgtaaataaatccatggttgcataccttattcagttaag--tttacatagATTTAGGACTGAGGCAACCTCGGCTGGAAGGAGAAGAATACTTGGCTGTTGTAGATGAATTCATGGAGGCTGTCCATGCACGTTGGCCTAAAGCAGTTGT

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G01680.1 (Glycine max), 3'ss of exon 7
---gtgcgtaagatacatcacacaacttctcaaactctttcactactttggagtaaattcctgtatcataacttaacttaccaagtatttcctt-----agATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT
    |   | | || ||  | || |   |  || ||      ||| |||    ||  |      |  |  | ||  |||       ||||   |     ||||||||||||  | ||||| ||||||||||| ||||| ||  | ||  ||||||||||||| ||||||||||||||||| || ||||| || ||  ||||
tttttttctcaaatgcaa-agaccataccaaaagctagcatgctaatttttgttagttgatatcagaaggaattggcttttttcacattttaatgtggcagATTTAGGACTTCGACAACCAAGGCTGGAAGGTGAAGAGTATCTATCAATTGTAGATGAATTTATGGAAGCTGTTCATGCTCGATGGCCCAAGGCTATTGT

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G08110.1 (Glycine max), 3'ss of exon 6
---gtgcgtaagatacatcaca---caacttctcaaactctttcact--actttggagtaaattcctgtatcataacttaacttaccaagtatttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT
    |||  |    | | || |    | | |   ||  | ||| | |  |  |  ||   ||||    | |  | | ||   | ||    || |     ||||||||||||  | ||||| ||| ||||||| ||||| ||  | ||  || |||||||||||||||||||||||||||| || ||||| || ||  ||||
caaatgcaaagatcataccaaaagctagcatgctaattttttttagttgatatcagaaggaattggc-ttttttgagttttttcacattttaatgtggcagATTTAGGACTTCGACAACCAAGGTTGGAAGGTGAAGAGTATCTATCAATTATAGATGAATTCATGGAAGCTGTTCATGCTCGATGGCCCAAGGCTATTGT

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 6
--------gtgcgtaagatacatcacacaacttctcaaactctttcactactttggagtaaattcctgtatcataacttaacttaccaagt-atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT
        | |       |  |  || |||  |   ||     ||   | ||||  || |||  ||   |  ||  |||  |  |  |  | | ||    ||||||||||||  ||||||||||  ||||||||||||| ||  | || ||||| |||||||| ||||||||| ||    | |||||||| || ||  ||||
ctagaataggggaatgtgtgaactacgcaaagtactaattaactt--gttctttccagcaaacaccataaggatttcttttcacatgactttagtttgacagATTTAGGACTTCGGCAACCTAGATTGGAAGGAGAAGAGTATCTATCAGTTGTTGATGAATTAATGGAAGCTATTTTCACTCGTTGGCCCAAGGCTATTGT

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|58687567|gb|CK076254.1|CK076254
EST:     ATGCTTGACGTNTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: ATGCTTGACGT-TGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|58673493|gb|CK062179.1|CK062179
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|58665242|gb|CK053928.1|CK053928
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|58694574|gb|CK083261.1|CK083261
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|88414501|gb|CI698600.1|CI698600
EST:     TATGCTTGACGTTGGAACAAATAACGCAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|58659006|gb|CK047686.1|CK047686
EST:     TATGCTTGACGTTGGAACAAATAACGCAGAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|88592463|gb|CI710566.1|CI710566
EST:     TATGCTTGACGTTGGAACAAATAACGCAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|29664101|gb|CB660376.1|CB660376
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|29671880|gb|CB668155.1|CB668155
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|29624067|gb|CB629078.1|CB629078
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|29656255|gb|CB652530.1|CB652530
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|29687359|gb|CB683634.1|CB683634
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|88342733|gb|CI677737.1|CI677737
EST:     TATGCTTGACGTTGGAACAAATAACGCAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|88386729|gb|CI682882.1|CI682882
EST:     TATGCTTGACGTTGGAACAAATAACGCAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|58604291|gb|CK014819.1|CK014819
EST:     GTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAAGCCTAGGCTGGAAGGAGAAGAATACTTGTCTGTT
genomic: GTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAA-CCTAGGCTGGAAGGAGAAGAATACTTGTCTGTT
EST: gi|29624065|gb|CB629076.1|CB629076
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
EST: gi|29678813|gb|CB675088.1|CB675088
EST:     TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTAT                         ATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG
genomic: TATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTG

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: 61 (upstream exon), 72 (downstream exon)
Score: 74

GTTCTTCCAATTATGCTTGACGTTGGAACAAATAACACAAAGCTTCTAGAAGACAAGCTATgtgcgtaaga ... atttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actactttggagtaaattcctgtatcataacttaacttaccaagtatttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT
                                 aacttac  putative branch site (score: 74)
                                            tatttcctt  putative PPT
                          ataacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtaagatacatcacacaacttctcaaactctttcactactttggagtaaattcctgtatcataacttaacttaccaagtatttccttagATTTAGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT