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'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatcgttgtactttccctctacctggatacctttgccttctcatcgcctttaatctcagttatttgtactttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATAGCCCGTGTGGAAGAGCTACAGTTCCTGGCAAGGCGCATTGCACGTTACA

Basic information

species Oryza sativa
transcript LOC_Os07g46590.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 27
gtataatcgttgtactttccctctacct---ggatacctttgccttctcatcgcctttaatctcagttatttgtactttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATAGCCCGTGTGGAAGAGCTACAGTTCCTGGCAAGGCGCATTGCACGTTACA
   ||||   | | ||||   |  ||      |||   ||||     |||||    ||||  ||| || |  | ||||  |||  |||||||||| ||||||||||| |||||||| || |||||  |||| ||| |||| ||||| |||||||| |||||| |||||| ||| |||||||||||||
--gtaataactctcctttttgttaactctaaagattattttgtgacatcatctttgttaagttcacttgt--gcacttccaatatagGGCACAGTTTTGGATTTTTTCGGTGTAGCTGTAAAGGCCTATGAATTGCTAGCTCGTGTTGAAGAGCTTCAGTTCTTGGCAAAGCGAATTGCACGTTACA

upper sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 22
-------gtataatcgttgtactttccctctacctggatacc-----------tttgccttctcatcgcctttaatctcagttatttgtactttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATAGCCCGTGTGGAAGAGCTACAGTTCCTGGCAAGGCGCATTGCACGTTACA
        ||| |  ||  ||  |  |  ||   |||  ||            ||      |||| |    ||||  ||| || |  | ||||  |||  |||||||||| ||||||||||| |||||||| || |||||  |||| ||| |||| ||||| |||||||| |||||  || ||| |||||||||||| ||||
aatacagatatcaaggtaataactctctcctttttggtaactgtaaagagtatttcatgacctcacctttgttaagttcacttgt--gcacttccaatatagGGCACAGTTTTGGATTTTTTCGGTGTAGCTGTGAAGGCCTATGAATTGCTAGCTCGTGTTGAAGAGCTTCAGTTGTTGTCAAAGCGCATTGCACGATACA
















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|87014366|gb|CI305144.1|CI305144
EST:     TACTCATTGAGGGTTGTCAAGATGCTGTTAAAAATAATATGGATGCCAAG                         GGCACAGTGTTGGANNNNNNNGGTGTAGCAGTTAAGGCGCATGAGTTGATA
genomic: TACTCATTGAGGGTTGTCAAGATGCTGTTAAAAATAATATGGATGCCAAGgtataatcgt ... ttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATA
EST: gi|86851021|gb|CI311239.1|CI311239
EST:     TACTCATTGAGGGTTGTCAAGATGCTGTTAAAAATAATATGGATGCCAAG                         GGCACAGTGTTGGA
genomic: TACTCATTGAGGGTTGTCAAGATGCTGTTAAAAATAATATGGATGCCAAGgtataatcgt ... ttaaatgcagGGCACAGTGTTGGA
EST: gi|29614085|gb|CB619098.1|CB619098
EST:     TACTCATTGAGGGTTGTCAAGATGCTGTTAAAAATAATATGGATGCCAAG                         GGCACAGTGTTGGANNNNNNNGGTGTAGCAGTTAAGGCGCATGAGTTGATA
genomic: TACTCATTGAGGGTTGTCAAGATGCTGTTAAAAATAATATGGATGCCAAGgtataatcgt ... ttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATA

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: 57 (upstream exon), 62 (downstream exon)
Score: 14

TGGTGCAATAGCAAAGTCTTCGGTTGATCAACAGCTTGAGCTGTTTACTCTACTCATTGAGGGTTGTCAAGATGCTGTTAAAAATAATATGGATGCCAAGgtataatcgt ... ttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATAGCCCGTGTGGAAGAGCTACAGTTCCTGGCAAGGCGCATTGCACGTTACA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacctttgccttctcatcgcctttaatctcagttatttgtactttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATAGCCCGTGTGGAAGAGCTACAGTTCCTGGCAAGGCGCATTGCACGTTACA
                      ctttaat  putative branch site (score: 14)
                                  ttatttgtactttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatcgttgtactttccctctacctggatacctttgccttctcatcgcctttaatctcagttatttgtactttaaatgcagGGCACAGTGTTGGATTTTTTTGGTGTAGCAGTTAAGGCGCATGAGTTGATAGCCCGTGTGGAAGAGCTACAGTTCCTGGCAAGGCGCATTGCACGTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT