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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcccttttttcaattgattacttggttgtgatatttgtagttgctaattttagtttatttttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC

Basic information

species Glycine max
transcript GLYMA01G29470.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------------------------------------gtatggcccttttttcaattgattacttggttgtgatatttgtagttgctaattttagtttattt--ttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC
                                                                                              ||   |     ||| |  || |  |  |  ||  |  | |   | ||  | | | |  |   ||   |||||| ||||||| ||||||||||| || || ||||| |||||| | ||  | || ||||| ||||||||||| |||||||| |||  ||| || |||||||| || |
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
---------------------gtatggcccttttttcaattgattacttggttgtgatatttgtagttgctaattttagt--ttatttt----tttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC
                     | ||  || |||   |  |   || |||  || ||| |  ||  ||| ||  ||  |    ||| |||     || | ||||||| ||||| ||||| || |||||||| |||||| ||||  | ||||| ||||| || |||||||||| |||||||  ||| ||||||||||| ||| 
aggcaacaccaccagcaaatggcataaccttttgcact-tcagtttctttattttgaaagatgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 15
----------gtatggcccttttttcaattgat-tacttggttgtgatattt--gtagttgctaatt-----ttagtttatttttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC
            |||   || |||| |||  || |||   |   ||||  ||   ||||  || |||     | | |  || ||  |   ||||||| ||||| ||||||||| ||||||| || ||| | || || ||||| ||||||||||||||||| ||||| ||| | ||||| || ||||| || |
gtaaaaagggagatgatgctgttttgaatatatctacactgacttgattattccatagtatctgattggctgtgattgcatgttggttacagATTGGTCTGGCTATGTCTCCTCTGAGCAACAATTCCTTGTTTTTGGACTATCATCGGAATCCTTTTCCTATGTTTTTCCTTCGGGGCCTCAATGTTTCCC

upper sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------------------------------------------gtatggcccttttttcaat-tgat-tacttggttgtga----tatttgtagttgctaattttagtttatttttttatt---agATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC
                                                       |  |  || |  |  |   |||  ||   || ||  |    ||| | |     || || |   | |  || |  |||   |||||||  |||| ||||||||||| ||||| |||||||| ||| ||||||||||||| |||||||| || |||||||| |  || ||||| || || ||  
gtgtggcactcttcctctaagattattgcttgatctttactctccgtctctcagatgagatccatcatatagggtgacataaccgggtgaaagatatatctatcacgactcatatgtttctcattatcgatttacagATTGGATTGGCCATGTCTCCTTTAAGCAACAACTCCCTTTTCCTAGACTACCATCGCAATCCTTTCCCCATGTTCTTTTCTCGAGGTCTCAACGTATCGT

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|9565158|gb|BE474667.1|BE474667
EST:     TCAATTTGAAAAAATCTCCCGTGCTTCAATATTTATATTATTTAGCCCAG                         ATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTAC
genomic: TCAATTTGAAAAAATCTCCTGTGCTTCAATATTTATATTATTTAGCCCAGgtatggccct ... tttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattacttggttgtgatatttgtagttgctaattttagtttatttttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC
                           tgctaat  putative branch site (score: 2)
                                       tttatttttttatt  putative PPT
                atatttgtagttgcta  TA-rich tract