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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcgatctctatacatgcacacaatatttatacacatgagtcatgatagtcatcctttccttctcttttcccccacatttctcactactgcactttctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC

Basic information

species Oryza sativa
transcript LOC_Os01g67340.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
--------------gtctcgatctctatacatgcacaca-atatttatacaca--tgagtcatga-tagtcatcctttccttctcttttc-ccccacatttctcacta-ctgcactttct-----cgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC--
               ||||  ||    ||  ||||| || || |  | | ||   ||| |||||| ||    ||   | |||   | | |     |   ||  || || | |  | | ||     |  ||||||||| ||| ||||| ||| ||||||| || || |||||||||||| | ||||| ||||||||||| || || ||  |    ||||| || |  |||   |  
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGA--AGTCTCCTG

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 8
--------------------gtctcgatctctatacatgcacacaatatttatacacatgagtcatga-tagtcatcctttccttctcttttc-ccccacatttctcacta-ctgcactttct-----cgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC--
                     ||    |   |  ||| |||||    |   | || | ||| || ||| ||    ||   | |||   | | |  |  |   ||  || || |    |||  |     | || ||||||||||| ||||| ||  ||||||| || || |||||||||||| | ||||| ||||||||||| || || ||  |    ||||| || |  |||   |  
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGA--AGTCTCCCG

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
gtctcgatctctatacatgcacacaatatttatacacatgagtcatgatagtcatcctttccttctcttttcccccacatttctcactactgcactttctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC--
|| |     ||     ||       | | ||  |   || |  | ||  |  |   |||||       |  ||   | ||         |     | |  || | ||||| || || || ||||||||||| || ||||| ||| | |||||| | |||||||||||||||||||| || ||| |    ||| || | |   || | |  
gtataagcttc-----atctttttgacagtttaatctataacccctgcgaaac-cactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGA--GGTCATCAA

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 6
gtctcgatctctatacatgcacacaatatttatacacatgagtcatgatagtcatcctttccttctcttttcccccacatttctcactactgcactttctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAG-TAAGC--
             || ||| ||| ||  ||  ||  |||   | |  |||    |  |   |  | |||     | | | |      |       |      || |||||||||||||||||||| ||||| || ||||||||||| |||||| | ||||||||||||||||| || || ||| |   || || ||||   || | |||  
------------gta-atgaacagaaacttcctagtcat---tta-aataactctagtggaccccacttacaagctaaaatgtgtgttttgatggta----aatacagCTTGCAGCGGTTGCAGCGTTGTGTGTGCAATACGAAGCAGAGTTTAGGCCAAACATGAGCATTGTAGTAAAAGCTCT---TCAACCGCTCTTGAGGTCAGCAA

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
--gtctcgatctctatacatgcacacaatatttatacacatgagtcatgatagtcatcctttccttctcttttcccccacatttctcactactgcactttctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC-
   |||    |||| |   |           | |  ||||       | | ||  |         |  ||  |  |  ||  |    | |  ||         ||||||||| ||||| || |||||||| || || || |||||||||||||| || ||||| |||||||| || ||||||||| |    || ||  | | | |      
gtctctttgcctctctctctctctctctctctcacccacacacacactcacagaaaaa-------taactagtagctaactctgtgaattggtgggt------gatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCT-TTTAAAGGCTGCTG

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|87039301|gb|CI193923.1|CI193923
EST:     ACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAG                         CTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
genomic: ACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAGgtctcgatct ... ctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
EST: gi|29644034|gb|CB649041.1|CB649041
EST:     GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAG                         CTTGCAGCGGTTGCAGCATTGTGCGTACAATATGAAGCTGAGTTTCGCCCA
genomic: GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAGgtctcgatct ... ctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
EST: gi|88830237|gb|CI076493.1|CI076493
EST:     GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAG                         CTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
genomic: GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAGgtctcgatct ... ctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
EST: gi|86489312|gb|CI131945.1|CI131945
EST:     GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAG                         CTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
genomic: GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAGgtctcgatct ... ctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
EST: gi|88841590|gb|CI080846.1|CI080846
EST:     GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAG                         CTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
genomic: GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAGgtctcgatct ... ctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
EST: gi|86498509|gb|CI141142.1|CI141142
EST:     GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAG                         CTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
genomic: GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAGgtctcgatct ... ctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
EST: gi|86427244|gb|CI072341.1|CI072341
EST:     GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAG                         CTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA
genomic: GTATAGATCCACGGTTGAATGGTGAATACCCACCAAAAGGAGTTGCCAAGgtctcgatct ... ctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctttccttctcttttcccccacatttctcactactgcactttctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC
                           ttctcac  putative branch site (score: 2)
                                       cactttctc  putative PPT