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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcctccttaagtcttccgtctggtatgtttttgtcattttgacatgcttaccaaatgtgttttttttttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACT

Basic information

species Oryza sativa
transcript LOC_Os12g03190.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 4
----------------------------gtaatgtcctccttaagtcttccgtctggtatgtttt-tgtcattttgacat-gcttaccaaatgtgttttttttttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACT
                             ||||   ||     | |         |   ||  |  |||  || |   ||   ||| ||| |   |||  | ||   |||||||||||||  | |||||||| |||||||||||||| || |||||||||||||||
gtaatactatttgacttgctcttctctgataatactctttcctaatgccagaatcgcactgcctcatgttgttctctgattaattaacaagtacatttgatgttgt-tgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT
















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|700649|gb|D46940.1|D46940
EST:     GTGGATGTTGTGTTGTATTGGCAAACAAGAAACCGCTTACTTGTGCTTAT                         GAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGANATTTGAATCT
genomic: GTGGATGTTGTGTTGTATTGGCAAACAAGAAACCGCTTACTTGTGCTTATgtaatgtcct ... tttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCT
EST: gi|702505|gb|D48796.1|D48796
EST:     GTGGATGTTGTGTTGTATTGGCAAACAAGAAACCGCTTACTTGTGCTTAT                         GAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCT
genomic: GTGGATGTTGTGTTGTATTGGCAAACAAGAAACCGCTTACTTGTGCTTATgtaatgtcct ... tttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCT
EST: gi|6481237|gb|AU065815.2|AU065815
EST:     GTGGATGTTGTGTTGTATTGGCAAACAAGAAACCGCTTACTTGTGCTTAT                         GAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCT
genomic: GTGGATGTTGTGTTGTATTGGCAAACAAGAAACCGCTTACTTGTGCTTATgtaatgtcct ... tttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCT

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: 54 (upstream exon), 41 (downstream exon)
Score: 42

TTGTTCTGCAACTTATGATACTGTTGGCATGCTAAAGGATGCCGTGGATCGTGGATGTTGTGTTGTATTGGCAAACAAGAAACCGCTTACTTGTGCTTATgtaatgtcct ... tttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatgtttttgtcattttgacatgcttaccaaatgtgttttttttttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACT
                       tgcttac  putative branch site (score: 42)
                                  tgtgttttttttttc  putative PPT
                               aaatgtgttttttttt  TA-rich tract