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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttaatttttagataatgtaccagatgcattatttgaaatcattcatgcaaaaagtataggatcgagggatacaagttactttaatgatcatttgtcaccttttaattcttcacacagGAGCACACATTGGACCAGAGCCTACAACTGACAGATTTGTTGTTGTCATG

Basic information

species Glycine max
transcript GLYMA07G39450.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39450.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
gttggttaatttttagataatgtaccagatgcat--tatttgaaatcattcatgcaaaaagtataggatcgagggatacaagttactttaatgatcatttgtcaccttttaa----ttcttcacacagGAGCACACATTGGACCAGAGCCTACAACTGACAGATTTGTTGTTGTCATG
||        |   | ||  ||| ||   | | |  ||||   ||| ||   | |         |   ||     | |||  || | || |  |  || |  ||   | | |    ||  ||   |||| || || ||||| |||||||||||||||||||||||||||||| | |  
gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttc--------cattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT

upper sequence: GLYMA07G39450.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0516g00020.t01 (Vitis vinifera), 3'ss of exon 10
gttggttaatttttagataatgtac-cagatgcattatttgaaatcattcatgcaaaaagtataggatcgagggatacaagttactttaatgatcatttgtcaccttttaattcttcacacagGAGCACACATTGGACCAGAGCCTACAACTGACAGATTTGTTGTTGTCATG
                     |||   | |     | |||    || | | |     |  || |   | |  |   |||| ||  |||  ||      | |  |||| |     ||   | |||||| ||||||||||||||||||||||| ||  | |||||||||||||||
---------------------gtaagtaaactttctgtttctgttcttccctttttcagttacaac-tagttgagaacaatttcgtttcttggcttactatttccttct----ttttggatagGAGCTCACATTGGACCAGAGCCTACAACCGATCGTTTTGTTGTTGTCATG
















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|298197514|gb|HO044993.1|HO044993
EST:     CACAGGGAAAACAACCTTCATAAAACATTTACTAAGATGTGATTATCCAG                         GAGCACACATTGGACC
genomic: CACAGGGAAAACAACCTTCATAAAACATTTACTAAGATGTGATTATCCAGgttggttaat ... cttcacacagGAGCACACATTGGACC
EST: gi|151413214|gb|EV283022.1|EV283022
EST:     CACAGGGAAAACAACCTTCATAAAACATTTACTAAGATGTGATTATCCAG                         GAGCACACATTGGACCAGAGCCTACA-CTGACAGATTTGTTGTTGTCATG
genomic: CACAGGGAAAACAACCTTCATAAAACATTTACTAAGATGTGATTATCCAGgttggttaat ... cttcacacagGAGCACACATTGGACCAGAGCCTACAACTGACAGATTTGTTGTTGTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagggatacaagttactttaatgatcatttgtcaccttttaattcttcacacagGAGCACACATTGGACCAGAGCCTACAACTGACAGATTTGTTGTTGTCATG
                                     ttttaat  putative branch site (score: 3)
                                   ccttttaattcttc  CT-rich tract
                 tttaatgatcattt  TA-rich tract