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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatattttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG

Basic information

species Oryza sativa
transcript LOC_Os05g23620.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 4
gtaatgatattttatgccattggcgttgcattgtt-taatcttccaccttcaagttgtaatttactgtttg-actccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
||||| | |  | ||    || ||  ||   |||| | ||||||||         | |   ||||||||   | | |     ||||||||||||||||||| ||||||||||| || |||||||||||||| || | |||||||||||| |||||||||
gtaattacagctaattt--tttgcagtgatctgttgtgatcttccattgc----gtatggcttactgttcacaatgcaatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 4
gtaatgatattttatgccattggcgttgcattgtt-taatcttccaccttcaagttgtaatttactgtttg-actccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
|||||   | || |||   ||| | |||| ||| | |   ||| |||       || |   |||||||||| | | | |   | ||||||||||||||||| ||||||||||| || |||||||||||||| ||||||||||||||||| |||||||||
gtaattgcagttaatggtgttg-cattgctttgatgtggcctttcact----gattatggcttactgtttgcattgcattcatccagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G06700.1 (Glycine max), 3'ss of exon 5
gtaatgata----ttttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
|||||| ||    ||| ||   | || | ||| | | ||  |   |    || |  |   ||  |  |  | ||| |       |||||||  | |||||||| ||||||||||| ||||| ||||| |||||||| ||||| |||||||| ||||||  |
gtaatgctaattatttgatagtaatgtctttggaattttctaatgtatgtctacctgaaatatatatccttgtgattt------ttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGTGACCCACCTGCTGGTGTTTCG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
gtaatga-tattttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgtt-cagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
||||||| | |  | ||| | |  |||  | ||   |  ||||   | || |  |  ||| | |   ||| || |   ||||| |||||  | |||||||| ||||||||||||||||| ||||| |||||||| ||||| || ||||| ||||||  |
gtaatgagtgtagtctgctagtaacgt--ctttagattttcttttgcttttatatcataaataa---ttttacccttaatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 4
gtaatga-tattttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
||||||| | |  | ||| | |   |||      |||  |||    | || |  | | || | | | ||   ||   ||| |||||||  | |||||||| ||||||||||||||| | ||||| || ||||| ||||| || ||||| ||||||  |
gtaatgactgtagtctgctagtaatgtttttagattt--tctattgcttttatatcggaaataatt-ttacccttaatat-ttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGTGACCCTCCTGCTGGTGTTTCG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 4
gtaatgata----ttttatgccattggcgttgca-ttgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
|||||| ||    ||| ||   | |  | ||| | || | |||| |    |   |      ||  |  |  ||||| |       |||||||  | |||||||| ||||||||||| ||||| ||||| |||||||| ||||| |||||||| ||||||   
gtaatgctaattatttgatagtaatatctttgaaattttctaatgtatgtctacctgaaaatatatatccttttgattt------ttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCA

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 3
--gtaatgatattttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
   |  || | |||    ||||| |  |   |||    |||    |  ||  | | | |||    |  |||| ||   |   | |||||| | ||||||||||| || ||||| ||||||||  | |||||||| |||||||| ||||| ||  ||  |
gtttggtgctctttctctccatttgtatacaattagaaaattcatctact--atgatctaa---gcaatttggctattttcttccagGCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 4
--gtaatgatattttatgccattggcgttgcat-tgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
   |  || |  |   |  | ||  |    ||| |||   |   |     ||   ||| ||| |   | |     || |  | | |||||| | |||||||| |  |||||||| ||||| ||||| ||||||||||||||||| ||||| ||  |   |
gtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgcct-tccagGCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGTGATCCCCCTGCTGGCATATCG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 4
gtaatga-tattttatgccattggcgttgcattg---tttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
|||||   ||| || ||   ||||| |   || |   ||   |||      | |||||  ||  || || ||   ||       |||||||  | |||||||| || |||||||| ||||| || || ||||||||||||||||||||||| ||  ||  |
gtaatttctatgttctggt-ttggcttcttatggagattatgtctatgttatccaagtgatatcttgcttttgttctt------ttcagGCTCGCCACAATGGTCAAAACTATGTATTTGCACTGCTAACTGGTTACCGTGATCCACCTGCTGGCATTTCG

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 3
---gtaatgatattttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
    ||||  | || ||   |  | |  | | | ||  |     ||||||   |     ||| | ||| |||| |  |      ||||||  | |||||||| ||||| ||||| ||||||||| | ||||||||||||||||| || || ||||||   
gtattaattttgttatagatcccttg-atagaagtgaatggctgtccacccctaca--ataactgactctttgtcctc------tcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA

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|55408838|gb|CV721214.1|CV721214
EST:     CCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCG
genomic: CCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAAT-GGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCG
EST: gi|27547605|gb|CA765614.2|CA765614
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29655598|gb|CB651873.1|CB651873
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|58682709|gb|CK071396.1|CK071396
EST:     CAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: CAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|3768179|gb|AU032206.1|AU032206
EST:     AAATGGTGGGNNATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: AAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29659241|gb|CB655516.1|CB655516
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|86522378|gb|CI162584.1|CI162584
EST:     TTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTACTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: TTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGT-CTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|88844350|gb|CI005723.1|CI005723
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29670618|gb|CB666893.1|CB666893
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|5003486|gb|AU068635.1|AU068635
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29674160|gb|CB670435.1|CB670435
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAG
                                   gtttgac  putative branch site (score: 4)
                       ttgtaattta  TA-rich tract