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'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtataataattatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g07130.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 6
tagtataataattatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttcctaaacatgtctacttgcaaa-cagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
| ||  |||  |||| ||||    ||  ||   |  | ||| | ||| | ||| |||  || ||  |  | ||   || || || | ||||  |  | ||||||||||||||||||||||||||||| || || |||| ||||||||||||||||||||||||||| || |||||||| ||||||||||||||||| |||
tggtcaaatgcttatctgtttgaacaagtttctaaacttttct-tcagtccttgtttccaacagttggatctccatctgaaaatatttactcccgtatcagGTTGGCCTACCAGCTCGTGGTAAAACCTTCACTGCAGTTAAGCTTACAAGGTACCTTCGTTGGTTGGGCCATGAAACTAGACATTTCAATGTTGGGAAG

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 7
-tagtataataattatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttc--ctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
 | | | ||   | ||||    ||| |  | |  |    || |||    || ||  ||| ||||| | ||| | ||    |    |    |  ||  |   |||| || || |||||  | ||||||||||| || |||||||| |||||||| || |||||||||||||||||| | |||| ||| ||||||||||| |||
ctggcaaaaatgtcatttccatttgtagttcatcaaa-gttagtaaatttggtt--ttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
tagtataataattatttgttattgcatcttaagattcatttgtatcactgctta---ttttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
  ||||   ||  || |  |||| |    |    |||||     | | |   ||   |||| ||||  | ||||  ||  |||  |    | |||  |   |||| || || ||||| || ||||||||||| || |||||||| |||||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||
-ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaa--tttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
----tagtataataattatttgttattgcatcttaagattcatttgtatcactgctt----attttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
    | | | || || |       ||| |    |    ||||| |   | | |        || ||  |||    ||  | |   ||      | | |||      ||||  |  | |||||||| || || ||||  || |||||||| || ||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||
tacctggaaaaaaaaatgcc--acattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttcctt------agGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
----tagtataataat----tatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
    | | | || |||     |||   |  || | ||| |  ||  || |||  |     ||||| |||| | | | |||||  |||      | | |||      ||||  |  | |||||||| || || ||||  || |||||||| |||||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||
tacctggaaaaaaaatgccacattcccttctgta-cttcatcttatttagtaaaataaaatattt-gaaatgaataatttctaactagtttctttttctt------agGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
-tagtataataattatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttc--ctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
 | | | ||   | ||||    ||| |  | |  |    || |||    || ||  ||| ||||| | ||| | ||    |    |    |  ||  |   |||| || || |||||  | ||||||||||| || |||||||| |||||||| || |||| ||||||||||||| | |||| ||| ||||||||||| |||
ctggcaaaaatgtcatttccatttgtagttcatcaaa-gttagtaaatttgttt--ttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
--------------tagtataataattatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
               || |   |||||   | || ||||| || || ||||||||     ||   || | || ||||  |    || |     ||||  | ||  |     ||||||||| | |||||||| |||||||||||||| |||||||| |||||||| || ||||| ||||| |||||||| |||| ||| |||||||||||||||
gcaacttccagtaacagcaggttaattccat-ttgttgcacctaaaaattcattt-----accaattttgttaaaaatgaatggttgt-----aacaaatttatattt---cagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
tagtataataattatttgttattgcatcttaagattcatttgtatcactgctt----attttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
   || ||  |   | |   ||| ||   | |  |||   ||  | |     |      ||    |||||  ||  | | || ||| ||||    || |  |||||||||||||| ||||| || || |||||||| ||||||||||| || || || ||  | ||| | || ||||| |||| ||| |||||||||||||||
---tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgtta-catactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG

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|33381245|gb|CF196588.1|CF196588
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|58695801|gb|CK084488.1|CK084488
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29615976|gb|CB620988.1|CB620988
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29616011|gb|CB621023.1|CB621023
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29615974|gb|CB620986.1|CB620986
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29616051|gb|CB621063.1|CB621063
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|58688458|gb|CK077145.1|CK077145
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATNGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29612781|gb|CB617794.1|CB617794
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG

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: 75 (upstream exon), 70 (downstream exon)
Score: 10

CAGGCCATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgcttattttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
                             tcctaaa  putative branch site (score: 10)
                                        tctactt  putative PPT
      ttattttgaaaa  TA-rich tract