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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtttttctttttatgtctttgttttttcatcatattttgattatttgtgaaataaaccag

Basic information

species Glycine max
transcript GLYMA20G35600.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35600.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 5'ss of exon 9
ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtttttctttttatgtctttgttttttcatca--tattttgattatttgtgaaataaaccag--------------------------------------
|| || |||||| | ||||||||||| |||||||| || ||||||||  | |||||||| || |||||||||||||   | ||  | |||  | |||   | ||  | ||  | | |  | | |||    ||     ||                                       
ATAGATACAAAGGACATTCTTTTTATTTGTGGTGGTGCTTTTATTGACTTGGAGAAAACTATATCAGAGAGgtattgcatattgatctttgagacttacctattggaacaattgtctccaatgttttctcaaatcgtcatctaatgtatttgcacctgctttaatttttaaaaatcag

upper sequence: GLYMA20G35600.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 9
ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtttttct--ttttatgtctttgt----tttttcatcatattttgattatttgtgaa-ataaaccag--------------------------
|| || |||||  |||| |||||||||||||||||||||||| ||||| | || |||||||||||||| ||||||    ||||  |    |  |  | | ||    | ||| |||| ||     || | ||||   ||      |                          
ATAGATACAAAAGATATCCTTTTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAGgtatgcacttttaataacatggttccctggtaaaatctttgatcaaatgccttttgtgtgtgtgtatgtgtgtgtgtgcatgcgtgtttgtgtgtgtgtg
















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|193357635|gb|FK320201.1|FK320201
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|208311212|gb|GE102988.1|GE102988
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGANCACCAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAG
EST: gi|193344284|gb|FK312814.1|FK312814
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|208037307|gb|GD836174.1|GD836174
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|193425329|gb|FK388602.1|FK388602
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|17519864|gb|BM188906.1|BM188906
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|193354939|gb|FK322548.1|FK322548
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|193339490|gb|FK302737.1|FK302737
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAAATAATA
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAA-TA-T-
EST: gi|207809763|gb|GD781837.1|GD781837
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|193361573|gb|FK324355.1|FK324355
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
EST: gi|193400816|gb|FK368737.1|FK368737
EST:     TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG                         ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtt ... aataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAGgtattttgtttttctttttatgtctttgttttttcatcatattttgattatttgtgaaataaaccag

- - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - -  GGAGCA