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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA

Basic information

species Oryza sativa
transcript LOC_Os07g47100.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
----------------------------------------gttagttgaacaaattttgccatacctc--gagagagacctggattcaacgtgctaa-----------tgtaatgatc-ttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
                                         ||  ||  | | | | |  | | ||||  ||| |  ||||||   |  | |  |||           |||||| | | ||   |   |||||||||||| ||||||||||||| |||||| |||||||||| || |||||||| || || ||||||||||| || ||  ||||||| ||||||||||| ||||
gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 6
gttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatctta---accccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
||| |  | |  |  |||   | |           ||   | |   || ||||| | || ||| ||||   |     |  ||||| || ||||||||||||||||| ||  |||||||||| ||||| || || ||||||||||| |||||||||||| | ||||||||||| ||| | || |
gtttgaagcaatatatttttaaaattcttccttcaactaaggtatcac-tgctagt-tactgaacttataaatgatgatgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 5
gttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaa--------cagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
||| |  ||||||  | |||| |    ||  |     | | |  ||| |||  ||||    |  || |||    |||        ||||| || || |||||||||||||| ||  |||||||||| ||||| || || ||||||||||| |||||||||||  | ||||||||||| ||| |  | |
gtttg--gaacaatatgtgcctttttccgcaacgttgcagcaaccaaggtgtcaatgcttagtactgaacttataaatgatgttgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTGGTGCTTTTCAATGCAATCAAAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 5
gttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaa--------cagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
||| |  |||| |  | |||| |   |||  |   | | | |   || |||  ||||  | |  || ||     |||        ||||| || || |||||||||||||| ||  |||||||||| ||||| || || ||||||||||| |||||||||||  |||||||||| || ||| || | |
gtttg--gaacgatatgtgcc-tttttcgcaatgtagcagcaacgaaggtgtcaatgctaagtactgaatttataaatgatgttgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTTGTGCTTTTTAATGCAATAAAAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 6
gttagttgaacaaat-tttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatctta---accccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
     ||||| | || |||   | |           ||   | |   || ||||| | || ||| ||||   |     |  ||||| || ||||||||||||||||| ||  |||||||||| ||||| || || ||||||||||| |||||||||||| | ||||||||||| ||| | || |
---gtttgaaaatatattttttaaattcttccttcaactaaggtatcac-tgctagt-tactgaacttataaatgatgatgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagttgaacaaattttgccatacctcgagagagacc--tggattcaacgtgctaat--gtaatgatcttaacccc-------aaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
       ||||   ||||   | || |  | ||| |    |  | |  |  | |||||    ||| | |||   | |       ||   |||| || ||||| || ||||||||  | ||||||||||| || || || |||||||| ||||||||||| |||||  | ||||| ||||| ||| ||||||
---gtaagaactttttttctgaaacattcaaagatattattctactacattttctaatcaaaaattaacttgcacgctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 6
--------gttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatg--taatgatctta----accccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
         ||  |  ||||    ||    ||| |  | | |  |    |   |  |  |  |    |  || || |           | | |||| || ||||| || |||||||| ||  | |||||||| |||||||| || ||||||||||| ||||| || ||| ||||| | ||||||||  | ||||
gtaatgtgttttctccaacatgacttaaattactt--acaaaccctgaaacatagtggaccgaaagtttctgttcctgttgtgttgtgatatagGTTCTGAATCAAGACGAGACACCTTTGCTTTACAGTCTTGTATTCGGAGAGGGTGTTGTGAATGATGCAACGTCAGTTGTGGTCTTCAACGCGATTCAGA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 2
gttagttgaacaaatt-ttgccatacctcgagagagacctggattcaacgtgctaatg-taatgatcttaacccc------aaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
|| |  |||        ||  || |  |  | | || ||  || |||| |||  | |   ||  |   |    ||       | |||||| |||||||| ||||||||||| ||  | |||||||| ||||| || || || |||||||| ||||| |||||  ||||||| ||||| ||  | ||||
gtaatgtgattcgccaattagcagaagtacatacaggcccagaatcaaagtgtaattaacaaaaactcttgttcctttggtgatacagGTTCTCAATCAAGATGAGACACCTTTGCTTTACAGTCTTGTATTTGGAGAGGGCGTTGTGAATGATGCCACATCTGTTGTGCTCTTCAATGCTATTCAGA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 6
----------gttagttgaacaa--attttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
            |   | | |    ||  ||  |    |    || |||     ||| ||   || || ||   |    ||        ||||| || ||||||||||||||||||||  | ||||||||||| || || |||||||||||||| ||||| |||||  | ||||||||||| ||| | ||||
gtacagatggccttactaagctgtgatcctgttactagttctaagggacaacacttccaca-acttatttatccaatccaattgtg---cagGTGCTTAATCAGGATGAGACACCCTTACTCTACAGTCTGGTTTTTGGAGAAGGTGTTGTGAATGATGCCACATCTGTGGTGCTTTTCAATGCAATCCAGA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 5
-----gttagttgaacaaa--ttttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccc-caaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
     | ||  |   |||   | |     | | || | |  |      ||  ||| |       ||| | |   | |    |   ||||| |||||||||||||||||||| ||  | |||||||| || || || |||||||| || || ||||| |||||  |                       
gtatagatatcttctcaaggctgtgattctgcttccataatggggacaatagaacatttctgactaaagtttgcatctgatatggcagGTGCTCAATCAGGATGAGACACCTTTGCTATACAGTCTAGTCTTTGGGGAAGGTGTGGTAAATGATGCCACATCTGTG----------------------

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S233_97V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------gttagttgaacaaattttgccatacctcgagaga--gacctggattcaacgtgctaatgtaatgatcttaaccc-caaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
                    ||| | |  ||||||    |   |      |      |   ||          |||  ||  || |  |         |||| ||| | ||||||  ||| ||  | ||||||||||| |||||||| ||||| || |||||||||||||| ||  | || || ||    ||  | ||||
ttgtgaaccagttggcccagagtaggaataattttttgttgattaattttactacttttattttgttacatagatgctattttcgtggcatattgtgtagGTGCTCGACCAGGATTCGACTCCTATGTTGTACAGTCTAGTATTCGGAGAAGGCGTCGTGAACGATGCTACCTCTGTGGTTCTGTTTCGGGCTTTCCAGA

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|27549114|gb|CA767092.2|CA767092
EST:     TGTCTGCACATTGCAG                         GTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAA
genomic: TGTCTGCACATTGCAGgttagttgaa ... cccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAA




















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: 47 (upstream exon), 63 (downstream exon)
Score: 17

CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgttagttgaa ... cccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
                                      tcttaac  putative branch site (score: 17)
                           taatgtaat  TA-rich tract