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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaccgaactattacagatcatgacaatttgaacttacacctatataatcttgtcagctacttatcatgtagttttatcagaagagctgaactgacatagactctttccagATGGCCTCACTAATGGAAGTGTTTGGAGGAGGTTCATTTGAGATGAAAATCATGAATAAAGTTGGATGCCTAAATTATTCAGCCACACAGTGGGAATCAG

Basic information

species Oryza sativa
transcript LOC_Os08g38440.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g38440.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G433609_T02 (Zea mays), 3'ss of exon 9
gtaagttcaccgaact---attacagatc---atg-acaatttgaa-cttacacctatataatcttgtcagctacttatcatgtagttttatcagaagagct--gaactgacataga-----ctctttccagATGGCCTCACTAATGGAAGTGTTTGGAGGAGGTTCATTTGAGATGAAAATCATGAATAAAGTTGGATGCCTAAATTATTCAGCCACACAGTGGGAATCAG
|||||||||    |||   ||  || |||   ||  ||||||  |  | | ||| | |  ||  | || | |||| |||  ||| ||   |||| ||||| |   |||||||||  |     ||||| |||||||||||| || ||||| ||||||  |||||| || || || |||||  | ||| | |||||||||||||  || || || || ||||||||||||||||
gtaagttcaggtgacttgtatggcaaatctaaatatacaattgcagtcctgcacttgtgcaagttcgttaactacctatattgtggtcc-atcataagaggttgaaactgacattcatgtatctcttgccagATGGCCTCGCTTATGGAGGTGTTTCTAGGAGGATCCTTGGAAATGAAGGTAATGGAGAAAGTTGGATGCCAGAAGTACTCGGCTACACAGTGGGAATCAG

upper sequence: LOC_Os08g38440.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179351_T01 (Zea mays), 3'ss of exon 8
gtaagttcaccgaact---attacagatcatgaca---atttgaa--cttacacctatataatcttgtcagctacttatcatgtagttttatcagaagag-ctgaa-ctgacataga-----ctctttccagATGGCCTCACTAATGGAAGTGTTTGGAGGAGGTTCATTTGAGATGAAAATCATGAATAAAGTTGGATGCCTAAATTATTCAGCCACACAGTGGGAATCAG
|||||||||    |||   ||  || |||   | |   | ||| |  | | ||| | |  ||  |  | | |||| |||  ||| ||   |||| ||||| ||||| |||||||  |     ||||| |||||||||||| || ||||| ||||||| |||||| || || || |||||  | ||| |||||||||||||||  || || || || ||||||||||||||||
gtaagttcaggcgacttgtatggcaaatctaaatatacacttgcagtcctgcacttgtgcaagttcattaactacctatattgtggtcc-atcataagaggctgaaactgacattcatgtatctcttgccagATGGCCTCGCTTATGGAGGTGTTTGCAGGAGGATCCTTGGAAATGAAGGTAATGGATAAAGTTGGATGCCAGAAGTACTCGGCTACACAGTGGGAATCAG

upper sequence: LOC_Os08g38440.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G149122_T02 (Zea mays), 3'ss of exon 9
gtaagttcaccgaact---attacagatcatgaca---atttgaa--cttacacctatataatcttgtcagctacttatcatgtagttttatcagaagag-ctgaa-ctgacata-----gactctttccagATGGCCTCACTAATGGAAGTGTTTGGAGGAGGTTCATTTGAGATGAAAATCATGAATAAAGTTGGATGCCTAAATTATTCAGCCACACAGTGGGAATCAG
|||||||||    |||   ||  || |||   | |   | ||| |  | | ||| | |  ||  |  | | |||| |||  ||| ||   |||| ||||| ||||| |||||||       |||||| | |||||||||| || ||||| ||||||| |||||| || || || |||||  | ||| | |||||||||||||  || || || || ||||||||||||||||
gtaagttcaggcgacttgtatggcaaatctaaatatacacttgcagtcctgcacttgtgcaagttcattaactacctatattgtggtcc-atcataagaggctgaaactgacattcatgtaactcttgctagATGGCCTCGCTTATGGAGGTGTTTGCAGGAGGATCCTTGGAAATGAAGGTAATGGAGAAAGTTGGATGCCAGAAGTACTCGGCTACACAGTGGGAATCAG

upper sequence: LOC_Os08g38440.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G149122_T01 (Zea mays), 3'ss of exon 9
gtaagttcaccgaactattacagatcatgacaatttgaacttacacctatataatcttgtcagctacttatcatgtagttttatcagaagag-ctgaa-ctgacata-----gactctttccagATGGCCTCACTAATGGAAGTGTTTGGAGGAGGTTCATTTGAGATGAAAATCATGAATAAAGTTGGATGCCTAAATTATTCAGCCACACAGTGGGAATCAG----------------------------
                                                    ||  |  | | |||| |||  ||| ||   |||| ||||| ||||| |||||||       |||||| | |||||||||| || ||||| ||||||| |||||| || || || |||||  | ||| | |||||||||||||  || || || || ||||||||||||||||                            
---------------------------------------------------caagttcattaactacctatattgtggtcc-atcataagaggctgaaactgacattcatgtaactcttgctagatggcctcgcttatggaggtgtttgcagGAGGATCCTTGGAAATGAAGGTAATGGAGAAAGTTGGATGCCAGAAGTACTCGGCTACACAGTGGGAATCAGATAAACCCAATGAGTATCAACGACATAT

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|27577936|gb|CB000631.1|CB000631
EST:     CAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAAT                         ATGGCCTCACTAATGGAAGTGTTTGG
genomic: CAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcac ... ctctttccagATGGCCTCACTAATGGAAGTGTTTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacttatcatgtagttttatcagaagagctgaactgacatagactctttccagATGGCCTCACTAATGGAAGTGTTTGGAGGAGGTTCATTTGAGATGAAAATCATGAATAAAGTTGGATGCCTAAATTATTCAGCCACACAGTGGGAATCAG
                                 aactgac  putative branch site (score: 2)
                                             ctctttcc  putative PPT
             tagttttat  TA-rich tract