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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA

Basic information

species Oryza sativa
transcript LOC_Os07g47100.3
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






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA
                                      tcttaac  putative branch site (score: 2)
                           taatgtaat  TA-rich tract