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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG

Basic information

species Glycine max
transcript GLYMA05G07020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
gtaatgagtgtagtctgctagtaacgtctttagattt--tcttttgcttttatatcataaataat--tttacccttaatgt---ttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
|| |       |   ||||   |    | |  | |    | | |    | || ||  ||  |||   |||    || |  |   |||||||  | |||||||| ||||||||||| ||||| ||||| |||||||||||||| || |||||||||||||||
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 4
gtaatgagtgtagtctgctagtaacgtctttagattt--tcttttgcttttatatcataaataat--tttacccttaatgt---ttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG----------------------------
|| |       |   ||||   |    | |  | |    | | |    | || ||  ||  |||   |||    || |  |   |||||||  | |||||||| ||||||||||| ||||| ||||| |||||||||||||| || |||||||||||||||                            
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGGTAACCCTCTCTCATACATATTGTTTTG

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

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

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 4
gtaat-gagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
||||| |    || |    | | |  |  || |  |   ||||  ||  | |||     |   |||       | |  | |||||  | |||||||||||||||||||| || || ||||| ||||| || ||||| || ||||||||||||  |
gtaattgcagttaatggtgttgcattgctttgatgtggcctttcactgat-tatggcttactgtttgcattgcattcatccagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 4
gtaatgagtg-tagtctgct--agtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
||||| |  | || | |  |  ||| |  | ||  ||| |||  |||| | |   | |    | |   | |    |||  |||||||  | |||||||||||||||||||| || || ||||| ||||| |||| ||| || ||||||||||||  |
gtaattacagctaattttttgcagtgatctgttgtgatcttccattgcgtatggcttactgttcacaatgc----aatcattcagGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 3
--gtaatgagtgtagtctgctagta-acgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
   |  ||    |  ||| |   |  |     |||||   |   |  ||  |||    |||  |||||  |  ||  | || ||||| ||||||||||| || || ||||| ||||| ||  | |||||||||||||| |||||||||||  |||||
gtttggtgctctttctctccatttgtatacaattagaaaattcat--ctactatgatctaagcaatttggctattt-tcttccagGCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 4
-------gtaatgagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttaccctta-atgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
       |     | | || | |    | ||| ||| |||     ||| || |||| | |  |||||| |||||   ||     || ||||| |||||||||||||  |||||||| ||||| ||||| |||||||| ||||| || ||||||||  | |||
gtctgctgctgctactttactttaactg-aacatctgtag-caaacttgtg-ttttgtgttttaaatagttttaatgttctgccttccagGCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGTGATCCCCCTGCTGGCATATCG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 4
gtaatgagtgtagtctgctagtaacgtctt-tagattttcttttgcttttatatcataaataattttacccttaatgttt-cagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
|||||   | |  |||| |  |  | |||| | ||  || | |   | ||||   |   ||| | || |  ||  | ||| |||||||| ||||||||||| |||||||| |||||||| ||||||||||| ||||| || ||||||||  |||||
gtaatttctatgttctggtt-tggcttcttatggagattatgtctatgttatccaagtgata-tcttgcttttgttcttttcagGCTCGCCACAATGGTCAAAACTATGTATTTGCACTGCTAACTGGTTACCGTGATCCACCTGCTGGCATTTCG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgagtgtagtctgctagtaacgtctt--tagattttcttttgcttttatatcataaataattttacccttaatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
     |  |  | | || ||   |   |||  ||||  |   |     |  |   |   ||||| |    | ||    | |||||| || |||||||||||||| ||||| ||||| ||| |||||||||| ||||| ||||| ||||||||||| 
-----gtattaattttgttatagatcccttgatagaagtgaatggctgtccacccctacaataactgactctttgtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA

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|15285987|gb|BI469878.1|BI469878
EST:     GGTTTGCTAATGGAGGATTCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
EST: gi|16343642|gb|BI969237.1|BI969237
EST:     AATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: AATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
EST: gi|58018184|gb|CX704926.1|CX704926
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
EST: gi|8670252|gb|BE191359.1|BE191359
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttagattttcttttgcttttatatcataaataattttacccttaatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG
                                         ccttaat  putative branch site (score: 4)
      attttcttttgctttt  TA-rich tract