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

gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT

Basic information

species Oryza sativa
transcript LOC_Os03g49420.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 15
gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaa--------ttcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
|||||  ||| || || | ||   | |  |  |  ||   |   | |  || |||| ||||||        || || ||| |||||||||| |||||| |||||||||||||||||||||| |||||  |||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||
gtatggtttgtatctatgttgtattcgatttatgtatgcatt--tgttattcgatgctgttaacaatcttgtttatttctacagAGGCCCTATCCAGATTATACAATGTAATCAAACATCCTAATGCCCTGGATTTGGATAATGCAATGGCCTATGACAATGCTGTTTCTGCTCTTGGAAAAAT

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G28950.1 (Glycine max), 3'ss of exon 18
gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
|||    |||           | |||||  |   |    ||  ||    |   | ||||||  |   |  |||||||||| || || ||  || |   ||| ||| | ||||| |||||  |  | |  |||||||  ||||||||||||||||||||||| ||| | || |||||
gtactgcttgatccattaacaaactaggaaaaagctgtactatattgagtaacaagttgttgttggcttactgcagAGGCTCTTTCGAGGTTAAATGCTGTGATCCAGCATCCTAATGCTCTTCATTCAGATAATGTAATGGCATATGACAATGCTGTTTCCGCTTTGGGAAAAAT

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 16
-----gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatc----tgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
      |      | |  ||    |    |    | || | |  ||  |||| ||||   | |     ||  | |     ||||||||| || || ||  || |   ||| || |  ||||| |||||  |  | |  |||||    ||||||||||||||||||||||| |||||||| |||||
gttagttgcacaataccattttcttattttgttgtcgtgccttactatatatattttttggataaatgtttctgttctattgcagAGGCACTTTCAAGGTTAGATGCTGTGATAAGGCATCCAAATGCACTACATTCTGATAACATAATGGCATATGACAATGCTGTTTCAGCTCTTGGAAAAAT

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 16
gtatgtgttgcatttacggtg--agctaggctagttcatagctgaatatgttttgat-----gttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
||||||  | | |  ||  ||   |  ||   | ||| |     | | |  ||| |      ||| ||| ||    | | ||||||| || || || ||| |    |||||    ||||| |||||  || |    |||||||  ||||||||||| ||||||||||||||||| || |||||
gtatgttctacttgcacattgttgggaagttaatttcttttgctattgtcctttaactaacagttcttagttgccttgttcagAGGCTCTTTCAAGGCTAAATGTCGTAATACGGCATCCTAATGCACTGCAACCAGATAATGTAATGGCATATGATAATGCTGTTTCTGCTCTAGGAAAAAT

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|29681491|gb|CB677766.1|CB677766
EST:     GCATNTAGGCCTCACACTGGTG                         AGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACT
genomic: GCATTTAGGCCTCACACTGGTGgtatgtgttg ... atatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
                                    tgttaat  putative branch site (score: 3)
                                   ttgttaattcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT