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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