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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatgcatgcaattttaaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG

Basic information

species Glycine max
transcript GLYMA05G33980.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaatt-gaacatgctt-----gatat-attgaattatgca----tgcaattttaaatttat--ttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
                                               |       | || | |||  ||  | | || || || || ||  |  ||   || ||  ||| |      || ||  | | |||| |          ||||  | ||| |  ||   ||||||||||||||||||||||||||||||||||  | || || |||||||||||  |||| || || |||||| | ||||| ||||||||||||||||| |||||||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG

upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
gtaagcttcttttcttttaacatattttcttgggttctatata-atataagcaattgaacatgcttgatatattgaattatgcatgca--attttaaattta--tttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
                  |    ||  |||||   | |  ||| ||||    |    | ||   | ||||  || || |   | ||||  ||  |||| | |  | |  |||||||||||||| ||||||||||||||||||||| | || || |||||||| |||||||| |  || |||||| | |||||||| || ||||| || || |||||||
------------------atgccatgctcttgaactatcgatacatatgcttagcataccaatttggataatttcaaatgcacttgcaccatactaaactcaaatgtgttttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG

upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
gtaagcttcttttcttttaaca-tattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatg-catgcaattttaaatttat--ttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
            |  || |||| | | | | | |    | |  | | | |   ||  | | || || | | |||  ||     ||     || | ||| |    ||   ||||||||||||| ||||| ||||||||||||||| | ||||| |||||||| ||| ||||||| ||||||||| | ||||| ||||| ||||||||||| || ||||
------------tacttgaacagtgtgtacatag----tgtggagtttgatgtatc-agcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG

upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgct-tgatatattgaattatgcatgcaattttaaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
||||  | |  |||| |      ||||||||   || |  | ||  |     ||| | |||  | ||| |     |  |  |  |  ||      |||  |||| ||  ||||||| || ||||| |||||||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||
gtaaaatgcaattctct------attttctt---ttttgcaaaagttgtctgattca-catattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG

upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatgcatgcaattttaaatttatttcctttt--tgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
     |  ||||| | | ||    |  ||| |    |||| ||       ||| ||  || | |       ||  ||||   ||   ||  ||| | || ||        | ||||| |||||||| ||||||||||||||| |||| ||||||||||| ||||||||    ||||||||  | |||||||| |||||||| || ||||||||||
-----ccacttttgtatgaaggcctgctctagttagctatcta-------caagtgtgcaggataag---gtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG

upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattga-acatgcttg-ata----tattga----attatgcatgcaattttaaatttatttccttt---ttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
                                 |    ||  |  ||   |  | | |   |   ||| | |||  | ||    ||||     || ||  |||    | ||||    |  |  |||   |   ||| | || |    ||   || ||||| |||||||| |||||||| |||||  | || ||||| ||||| ||||||||    || ||||| |||||||| |||||||| ||||||||||||||||
gtaagattctttttcaccaaacccaactactcttgctatttctccctaccaggaaaatgcttctagttttctattttgtagaatattgttgtgtggttctatagtgttgttgagaagaccagccatctcaagctaagtctactcttgttatatttcagTATACCCCTGCGATTGATATCTGGAGTGTCGGTTGCATTTTTGCGGAAATGCTTTTGGGTAAGCCTTTGTTTCCCGGGAAAAACGTTGTGCACCAATTGG

upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatgcatgcaattt--taaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
        |||||  |  || ||    |||| |||| |||| ||| ||||         ||| ||    |||| || |||  ||  |||||  ||||    | ||| |||| |||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| || || || ||  ||||||| ||||||||||| |||||||| ||||
--------cttttgatgaaatatgacctctttggtt-tataaaatttaagtgg--agttatgttt----tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG

upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ26549 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatgcatgcaattttaaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
                                                 | ||  | | ||   || |  |||   || || | ||       || | || || | | ||||||| || || ||||| || || ||||||||||| ||||||||||| || |   ||||| |||||||| |||||||||| || || |||   || ||  | |
-------------------------------------------------gtaagaggatat---tggttcatttttttctg-acgc------caagtgatctcttgtatgcagTATACTCCAGCAATCGACATATGGAGCATTGGTTGCATATTTGCTGAGACAATCACTCGGAAGCCACTGTTTCCTGGAAAGAACGTTACTCATCAGCTCG

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|192306378|gb|FG996138.1|FG996138
EST:     CAACTCGGTGGTACCGTGCACCTGAATTATGTGGTCCTTTTTTCTCAAAA                         TACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAA-TG
genomic: CAACTCGGTGGTACCGTGCACCTGAATTATGTGGTTCTTTTTTCTCAAAAgtaagcttct ... ctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcttgatatattgaattatgcatgcaattttaaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
   gcttgat  putative branch site (score: 5)
                                     tttatttcctttttgc  putative PPT
        atatattgaattatgc  TA-rich tract