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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaattacctttcttcatcatacttgtgctctggcggtaaaatatttgtacagaccatttcaagattaggaataaaattgatactgttttt...

Basic information

species Glycine max
transcript GLYMA15G09090.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09090.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaattacctttcttcatcatacttgtgctctggcggtaaaatatttgtacagaccatttcaagattaggaataaaattgata-ctgttttt---
||| |||||||||||| | ||||||||||| || ||||| ||| |||| ||||||||||||||||||||||| |||||||| || |||||||| || |||||||||     |   | | || |  | ||  |   |  | |||       | |||| ||   |||  |    |||    |  ||   | ||  ||| | |    
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgag--aacattttcaaacagtcgctttttatggt------acatttatatttacctgtcatggatgcttatcaatgctcatttctggtatgcag

upper sequence: GLYMA15G09090.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 5'ss of exon 11
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcc-ttaaattacctttcttcatcatacttgtgctctggcggtaaaatatttgtacagaccatttcaagattaggaataaaattgatactgttttt------------
||| |||||||||||||||||||||||||| || ||||| ||  |||| ||| ||||||| || ||||||||||| || ||||| ||||||||||| |||||||||   | | || |    |  ||  | |||      || |    |   ||   ||   | |    | |     | ||     | ||| | |||  |||            
TGATGCATGTGCACATCCTTTCTTTGATGAGCTGCGAGAGCCGAATGCACGCTTGCCAAACGGACGTCCATTTCCACCACTATTCAACTTCAAACACGAAgtaagtgaatcagatgaaacataatctgc-tacacaacttcagatcttggtatccatgagaaaatgtgtactctccttggtgctca-ttggtgctgccttttggtctctacag

upper sequence: GLYMA15G09090.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 11
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaattacctttcttcatcatacttgtgctctggcggtaaaatatttgtacagaccatttcaagattaggaataaa-attgatactgttttt---
 ||||||||||||||||||||||||||||| || ||||||||| |||| ||||||||||||||||||||||| || ||||| || || || || |||||||||||   ||  |||   | | || ||  |  || | || |     |   | | |  |        | || ||  |    ||     |  ||| | | ||    
AGAAGCATGTGCACATCCTTTCTTTGATGAGCTCCGAGAACCCAATGCCCGCCTGCCAAATGGTCGTCCATTACCACCTCTCTTCAATTTTAAGCAGGAAgtaagggtttttatt--ttatttttatattttttattctatataatttctaaactaattt--cttgtctccagcctgaacatgtctgtccataatttcttcatg

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|10253367|gb|BE821133.1|BE821133
EST:     GCCTGCCAAATGGTCGTCCATTTCNTNNNCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|10255492|gb|BE823258.1|BE823258
EST:     ATTTAACTTCAAACAGGAA                         TTANNTGAAGCATNNCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
genomic: ATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|254330723|gb|GR841988.1|GR841988
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|254329846|gb|GR839399.1|GR839399
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAACAA-TTGATACCTGACCACGTG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|7030035|gb|AW459818.1|AW459818
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|23731206|gb|BU763715.1|BU763715
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|12774190|gb|BG239117.1|BG239117
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|151404035|gb|EV273845.1|EV273845
EST:     CTCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
genomic: CTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG
EST: gi|193615193|gb|FK560613.1|FK560613
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAA                         TTATCTGAAGCATCTCCAGTGCTTGTTAGCAAATTGATACCTGACCACGTG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgttgacagTTATCTGAAGCATCTCCAGTGCTTGTTAACAAATTGATACCTGACCACGTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaattacctttcttcatcatacttgtgctctggcggtaaaatatttgtacagaccatttcaagattaggaataaaattgatactgttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaataaa