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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttaaacagctgtatgaaccacagttacttattttcactctgtcagtatctgatacttcagtacaatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTGTGGACAGCTGCTATTGTTTGCCTTATTGTAGCTTGGCCAAAAAGTAACT

Basic information

species Oryza sativa
transcript LOC_Os12g18110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g18110.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 3
--------gttagttaaacagctgtatgaaccacagttacttatt-ttcactctgtcagtatctgatact-tcagtac---aatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTGTGGACAGCTGCTATTGTTTGCCTTATTGTAGCTTGGCCAAAAAGTAACT
        | ||  | |    |  |   |    |   ||  | ||  | ||||    | | | |   | | ||   ||   || ||| |||||||||  |||||| |||||||||| |||||||||||  |||||||||| ||||  || ||| |||||||||| ||| | ||||||||||||||| |||
gttagtttgctatgttattgaccatgaaattttctcctagctgttactgactcctaaactcttttgaattatccaaaccgaaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTCTGGATCGCCGCTCTTGTTTGCCTCATTATTGCTTGGCCAAAAAGTGACT
















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|88693439|gb|CI737014.1|CI737014
EST:     ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAG                         CGAGGAAACCAGAAAATC
genomic: ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAGgttagttaaa ... caatatacagCGAGGAAACCAGAAAATC
EST: gi|88574642|gb|CI666411.1|CI666411
EST:     ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAG                         CGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCA
genomic: ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAGgttagttaaa ... caatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCA
EST: gi|9886160|gb|AU066053.2|AU066053
EST:     ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAG                         CGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTG
genomic: ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAGgttagttaaa ... caatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTG
EST: gi|56157764|gb|C26318.2|C26318
EST:     ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAG                         CGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTG
genomic: ACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAGgttagttaaa ... caatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTG

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: 74 (upstream exon), 48 (downstream exon)
Score: 115

ATGATTCCTGTCGCGGCAAATGATGTTGCCTTTTCTGTACACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAGgttagttaaa ... caatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTGTGGACAGCTGCTATTGTTTGCCTTATTGTAGCTTGGCCAAAAAGTAACT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacagttacttattttcactctgtcagtatctgatacttcagtacaatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTGTGGACAGCTGCTATTGTTTGCCTTATTGTAGCTTGGCCAAAAAGTAACT
                             atctgat  putative branch site (score: 115)
      ttacttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttaaacagctgtatgaaccacagttacttattttcactctgtcagtatctgatacttcagtacaatatacagCGAGGAAACCAGAAAATCTCCAAAGTCTGCATATCAATCACTGCTATTGTGTGGACAGCTGCTATTGTTTGCCTTATTGTAGCTTGGCCAAAAAGTAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT