Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatcgggaaaacctctcctgtaacttaccaagtgcttggccatctcaagacatgcttggttcttgcctttggttatgttttgcttcacgatccatttagCTGGAGAAATATACTTGGAATCCTCATTGCTGTGATTGGGATGGTATCGTACTCATACTTCTGCACAAAAGAGGCTCCACCAAAACCCACTGAAGCCTCC

Basic information

species Oryza sativa
transcript LOC_Os01g07310.4
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 6
tgatcgggaaaacctctcctgtaacttaccaagtgcttg-gccatctcaagacatgcttggttcttgcctttggttatgttttgcttcacgatccatttagCTGGAGAAATATACTTGGAATCCTCATTGCTGTGATTGGGATGGTATCGTACTCATACTTCTGCACAAAAGAGGCTCCACCAAAACCCACTGAAGCCTCC---
       | || | |         |||     | | ||| |  | ||   || ||   |   |||   | | |||     |||| | |     |  |||  |      |   | ||      ||| ||| | ||  | ||     |   | |||  | ||  ||  |   |     ||  |   |||| ||  |  |||     
-------gtaagcattagaccaggctt-tggggagtttgcgttaactgtcgatatcgctccatctgatcatgggtctgcatttgttgcctctgcagTTTTTC------ATCGTGCTGTCGTGCCTGATTTCAGTC-TCGGTGAACTTCAGCACTTTT-CTCGTGATCGGGAAGACGTCTCCTGTAACCTACCAAGTCCTTGGCC


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagacatgcttggttcttgcctttggttatgttttgcttcacgatccatttagCTGGAGAAATATACTTGGAATCCTCATTGCTGTGATTGGGATGGTATCGTACTCATACTTCTGCACAAAAGAGGCTCCACCAAAACCCACTGAAGCCTCC
                                   ttgcttcac  putative branch site 
                                              tccattt  putative PPT
                            ttatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatcgggaaaacctctcctgtaacttaccaagtgcttggccatctcaagacatgcttggttcttgcctttggttatgttttgcttcacgatccatttagCTGGAGAAATATACTTGGAATCCTCATTGCTGTGATTGGGATGGTATCGTACTCATACTTCTGCACAAAAGAGGCTCCACCAAAACCCACTGAAGCCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - -ctcctgt
- - - - - - - - - - - - - - - - gtgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - atgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcttc