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'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacattaaatgactttatgctggcataatctactgtggcatgctgtcctttaataagattgctcttttgttccaacaagtgttgtttatgtcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT

Basic information

species Oryza sativa
transcript LOC_Os03g15120.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 17
aacattaaatgactttatgctggcataatctactgtggcatgctgtcctttaataagattgctcttttgttccaacaagtgttgtttatgtcttttcca-gGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT
  | |  |||  ||||     |  |  |   |   | |   |   |      |     |      ||| |||  |    | ||  |||||| | ||  | ||| | ||| || || ||  |||| || || || || ||||||||||| ||||||||||||||  | |||||||| |||||||| ||||||||||||||||
ctcttggaatttcttttgaaggaaaagaatgaagatagttagtcatttgcctacttcctgaagtattttttcttatct-tattacttatgtttattgtaagGTTAATGGGGGACGAGAGGGCCGGCCAATTGGTGCTTATGAACTAGCAAAAGCAGTTGAAGAGCTTGGTGCTGGTGAAATACTACTTAATTGCATTGATT

upper sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 17
aacattaaatgactttatgctggcataatctactgtggcatgctgtcctttaataagattgctcttttgttccaacaagtgttgtttatgtcttttcca-gGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT
  | |  |||  ||||     || |  |   |   | |   |   |      |     |      ||| |||  |      ||  |||||| | ||  | ||| | ||| || || ||  |||| || || || || ||||||||||| ||||||||||||||  | |||||||| |||||||| ||||||||||| ||||
ctcttggaatttcttttgaagggaaagaatgaagatagttagtcatttgcctacttcctgaagtattttttcttatct-cattacttatgtttattgtaagGTTAATGGGGGACGAGAGGGCCGGCCAATTGGTGCTTATGAACTAGCAAAAGCAGTTGAAGAGCTTGGTGCTGGTGAAATACTACTTAATTGCATCGATT

upper sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 15
aacattaaatgactttatgctggcataatctactgtggcatgctgtcctttaataagattgctcttt-tgttccaacaagtgttgtttatgtc-ttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT
 |||||   | |||  |||     |  |   | | |   |    ||   ||  |||  ||    |||   ||  ||      || ||    |  || ||||||| | ||||||||| ||  |  | || || ||||| ||||| || || ||||||||||||||  |||| |||||||||||||| || || ||||||||||
-acattttct-actagatgaaaataggacacaatcttttacttggtgaattgttaactttttattttgcatttgaaatgacattcttccaatgattctccagGTTAATGGTGGGCGAGAAGGTAGACCAATTGGAGCTTATGAGCTTGCAAAAGCAGTTGAAGAGCTGGGAGCTGGAGAAATACTACTCAACTGCATTGATT

upper sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 14
lower sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 15
-aacattaaatgact-ttatgctggcata-atctactgtggcatgctgtcct-ttaataagattgctcttttgttccaacaagtgttgtttatgtcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT
  || | |  |      |   ||| | |  | ||  | |  | || | |  | |||||||   ||    | |  | ||   | |    || ||| | | || |||| || ||||| || |||||  | ||||||||||||||||| || |||||||||||| ||||  | |||||||| ||||| ||  | || |||||  |||
gtacttcacgttgtggcttccctgacttggaactcattttacgtgttttattattaataatcctgggtatcttatgcactgattccaattcatgccctgtc-agGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATT

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|86504136|gb|CI146769.1|CI146769
EST:     GAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
genomic: GAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
EST: gi|88907823|gb|CI091221.1|CI091221
EST:     GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
genomic: GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
EST: gi|87010113|gb|CI279210.1|CI279210
EST:     GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
genomic: GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
EST: gi|33808918|gb|CF330345.1|CF330345
EST:     AGGTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCCGTCCTATAGGAGCATATGAACTAGCCAA
genomic: AGGTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAG-CCGTCCTATAGGAGCATATGAACTAGCCAA
EST: gi|86500063|gb|CI142696.1|CI142696
EST:     GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAGA
genomic: GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
EST: gi|86432146|gb|CI085757.1|CI085757
EST:     GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
genomic: GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
EST: gi|88221798|gb|CI221754.1|CI221754
EST:     GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
genomic: GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
EST: gi|86597766|gb|CI274757.1|CI274757
EST:     GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
genomic: GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
EST: gi|87016640|gb|CI275642.1|CI275642
EST:     GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACA                         GTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA
genomic: GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAA

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: 69 (upstream exon), 73 (downstream exon)
Score: 16

GTCCATTAGGAGAAGAATATGCATGGTACCAGTGCACAgtaagccatt ... tcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttaataagattgctcttttgttccaacaagtgttgtttatgtcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT
  ctttaat  putative branch site (score: 16)
                                       tttatgtcttttcc  putative PPT
     taataagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacattaaatgactttatgctggcataatctactgtggcatgctgtcctttaataagattgctcttttgttccaacaagtgttgtttatgtcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - -tgctggc
- - - - - - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - ggcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt