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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGCGCAGGACCGCTACATCTTCCACGTCCTCCGCTCCCCTCCCCCCGCCGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAAgtacaaactctcttatacttactagtattactctactaatctatatgatctatggataggataagatggattcgttcattcatcttcttagtatgttctt...

Basic information

species Oryza sativa
transcript LOC_Os10g06540.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g06540.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 1
------------TTCGCGCAGGACCGCTACATCTTCCACGTCCTCCGCTCCCCTCCCCCCGCCGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAAgtacaaactctcttatacttactagt-attactctactaatctatatgatc-tatggataggata---agatggattcgttcattcatcttcttagtatgttctt
            |||||||||||||| |||||||||||||||||||| ||            || |||||  ||| ||||||||||||| |||||||||||||||||||||||||   || ||    | ||  | | |  ||  |   ||        || ||  ||  ||| |||    || ||     | |   |  |  ||  |||  |     
TCCAGGCTGTGCTTCGCGCAGGACCGGTACATCTTCCACGTCCTCCGATC------------CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactacccttcgttcctctcaattcgttcgttcgctcgctcgcttgctcgcatacataagatttttagctgctactgattgctagtactcc-agttggc----

upper sequence: LOC_Os10g06540.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA12G09680.1 (Glycine max), 5'ss of exon 1
TTCGCGCAGGACCGCTACATCTTCCACGTCCTCCGCTCCCCTCCCCCCGCCGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAAgtacaaactctcttatacttactagtattactctac-taatctatatgatctatggataggataagatggattcgttcattcatcttcttagtatgttctt----
| ||        | || | |||  || |  | |  |  |   | |     |    | |||||| |||||| | |||| ||||||||||||||||||||||||  |     |||| | |||  |    |    || | |||||    | ||||     |   ||       || || |  | | | |  |||  | ||   |    
TCCGACTCCAGGCTCTGCTTCTCTCAGGATCGCTACATCTTCCACATACTCCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtg-agttcttcttcttcttcttctcctcctccttcgtaatc---gtaatcttaatttcatatttatacaatccgatt-tacttttagttaagacgtagatgcta

upper sequence: LOC_Os10g06540.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA11G18760.1 (Glycine max), 5'ss of exon 1
TTCGCGCAGGACCGCTACATCTTCCACGTCCTCCGCTCCCCTCCCCCCGCCGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAAgtacaaactc--tcttatacttactagtattactctactaatctatatgatctatggataggataagatggattcgttcattcatcttcttagtatgttctt
| ||        | || | |||  || |  | |  |  |   | |     |    |||||||| |||||| | |||| ||||||||||||||||||||||||     ||   |||| | |||  || |  || |||  |||| |   || | || |    |  |    |  | |       |    |     | |   ||||
TCCGACTCCAGGCTCTGCTTCTCTCAGGATCGCTACATCTTCCACATACTCCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttcttcgtctttttcttcttaatcgtaatct--taatttcgttgttatacgatccgattctctttcagttaaaatgtaggatctactgaagagtctt

upper sequence: LOC_Os10g06540.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv06s0080g00800.t01 (Vitis vinifera), 5'ss of exon 1
TTCGCGCAGGACCGCTACATCTTCCACGTCCTCCGCTCCCCTCCCCCCGCCGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAAgtacaaactctcttatacttactagtattactctactaatctatatgatctatggataggataagatggattcgttcattcatcttcttagtatgttctt-
  ||        | ||   |||  || |  | |  |     || |     |   |||||||| ||| | ||||| |||||||||||||||||||||||||||    | ||     | |||  |  ||||  | || |  |   | | ||       |  | |  | | | ||  ||  || ||||     |   | |    
GCCGATTCCAGGCTCTGTTTCTCGCAGGATCGCTACATATTTCACATACTCAGAGCCGATGGACTCGCGTTCCTTTGCATGGCCAACGACACCTTCGGAAgtctgtagtcatcgcttcttcgttttatt-ttttaatttttggttttattataatttttgttttgttcggttttttggttgatctggcccgggagctaggg

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|218501230|gb|FG958972.1|FG958972
EST:     CGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAA                         GACGAATTCCCTTTCTTTACCTCGAGGACATCCAAATGAGGTTCATCAAGA
genomic: CGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAAgtacaaactc ... ttaattacagGACGAATTCCCTTTCTTTACCTCGAGGACATCCAAATGAGGTTCATCAAGA