Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC

Basic information

species Oryza sativa
transcript LOC_Os01g15460.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |||| ||      ||||| ||  || || | ||||  |||||||    || | |  ||   |  ||| |||||||||||||||| || ||||||||||| ||||| ||||||||||| || |||||  ||||||||||||| |||||||| ||||| |||||| |||||       
gtatgagaattctcctatggatgtgcttctttgta-acat-ttttaactgtttttgggaaaaaa--tttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCG-------

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |||| ||      ||||| ||  || || | ||||  |||||||    || | |  ||   |  ||| |||||||||||||||| || ||||||||||| ||||| ||||||||||| || |||||  ||||||||||||| |||||||| ||||| |||||| ||||| | ||||
gtatgagaattctcctatggatgtgcttctttgta-acat-ttttaactgtttttgggaaaaaa--tttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |||| ||  ||  || || ||        | ||||   | || |   ||| |    |||  |  ||| || ||||||||||||| || ||||||||||| ||||| ||||||||||| || |||||  ||||||||||||| |||||||| ||||| |||||| ||||| ||||||
gtatgagaattctcctatgattgtgtttcttgga-----ttttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G17250.1 (Glycine max), 3'ss of exon 4
gtgtgaaatctc-tcgtaaaatattgcttattcatac-acttgtttttcctgttttgaaaaag-agatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| |||    || |  |    |  |||| || |||   || |        |  |   |      | |   ||       |  ||  ||||||||||| ||||||||||||||  ||||||| ||||| || |||||||| |   | |||||||||||||||||  ||   | |||     |  || |  
gtatgactcttcgttttgctcttctgctcatccatgttacctacagaaaataatgcaattggttaaaccatgccttttgtttaa-acagGGTGAGAAAGAGTGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G02550.1 (Glycine max), 3'ss of exon 4
gtgtgaaatctctcgtaaaatat-tgcttattcatac-acttgtttttcctgttt-tgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| |||    |||  |      | ||||  |||||   || |        |   | | |  |  | |   ||       |  ||  ||||||||||| || |||||||||||  | ||||| ||||| || |||||||| |   | |||||||||||||||||  ||   | |||     |  || |  
gtttgactcttctttttgctcttctgctcgttcatgttacctacaccaaataaatgtaatgattaaaccatgccttttgtttaa-acagGGTGAGAAAGAATGCTCCTACTATTTAAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G28820.1 (Glycine max), 3'ss of exon 4
-------------------------------------gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                     |  ||   |     ||    | ||| ||  | || ||      | |  || |  ||    || |||||  || | || | |  ||||||||||||||||| ||||| ||  ||||||| || ||||| || |||||  | || ||||||||||||||||| |     | |||  | |  ||  | |
gtctgtatcactttttgtatttactacataaggctaggcatgcttttgaatgttctgttttgttttctgat-catggaaatattttgatccgagtttga-atgtttataaatatgata-acagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCATCCAAATTCCAC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
----------gtgtgaaatctct-cgtaaaatattgctta-ttcatacactt----gtttttcctgttttgaaaa----agagatgttggtacaaataaaat--------------gcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
          || ||   |  || ||||||||  ||  |  ||  |  | ||    ||   || | |  | |  |     ||  | ||| |  || |  |||               |||||| |||| ||||| ||||| ||| |||||||||| || || || |||||  | || |||||||||||||||||  |    |  || || |   |     
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G10230.1 (Glycine max), 3'ss of exon 4
----------------------------------gtgtgaaatctctcgtaaaatattgcttat----tcatacacttgtttt-tcctgttttgaaaaagagatgttggtaca-aataa--aatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                  |     | | | | || ||   |   || |    ||  ||| | |     |  || | ||||   || |||||  || |  ||||  |   ||||||||||||||||| ||||| ||  ||||||| || ||||| || |||||  | || ||||||||||||||||| |     | ||| || |  ||  |  
gtctgtgtcacttttttgaatttacttacataaggctaagagtgttttgtgaatgttcagttttgttttctgacagtggaaagattttgatctgaatttga-atgtttataaatgataatgataacagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCGTCCAAATTCCAG

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaa-gagatgttggtacaaataaaatg------cagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |  |      | |||||  |       || || |           ||  | |  |||||   |||       ||      ||||||||||| || |||||||||||  ||||||| ||||| || |||||||| |   | |||||||||||||||||  ||   | |||     |  || |  
gtatgataa-tgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
  || |  | | |    |   || |   | | | |  || || |   |   |||| |     ||| ||  || |||     || ||||||| || || |||||||||||  ||||||| |||||||| |||||||| |  || |||||||| ||||||||  |    | ||||  | |  |  | |
--gtaagctttgtttccactcat-gtcaaataaaaggctagtct---cgagtttgcat----gatcttt-tataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC------------------------------------------------------------------------------
  || |  | | |    |   || |   | | | |  || || |   |   |||| |     ||| ||  || |||     || ||||||| || || |||||||||||  ||||||| |||||||| |||||||| |  || |||||||| ||||||||  |    | ||||  | |  |  | |                                                                              
--gtaagctttgtttccactcat-gtcaaataaaaggctagtct---cgagtttgcat----gatcttt-tataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------gtgtgaaatctctcgtaaaatatt-gcttattcatacacttgtttttcctgttttgaaaaagag-atgttggtacaaataaaat------gcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                 | ||||   |  ||  | ||  || |  |  ||   | |   |      ||  |   ||   |||||  |  |    ||||       ||||||||||| || |||||||||||  ||||||| ||||| || || ||||| |  ||||||||||||||||||||  ||   | |||     |  || |  
gttgggatttggtttattcttcaccttttctaatcaaattcgttttactaaatcagcatggttgtaatttgggaatggacacttccatttagcttatgtttatgaattggaaattttgcaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAGTTTGGTATAACATGTAAATTCCATCATCCTCAACCAGCTGGCACATCATTGCCAG

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|88572959|gb|CI664530.1|CI664530
EST:     GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTG                         GGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
genomic: GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTGgtgtgaaatc ... taaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
EST: gi|88306285|gb|CI636670.1|CI636670
EST:     GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTG                         GGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
genomic: GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTGgtgtgaaatc ... taaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
EST: gi|88306241|gb|CI636626.1|CI636626
EST:     GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTG                         GGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
genomic: GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTGgtgtgaaatc ... taaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                       tacaaataaaat  TA-rich tract