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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGGACGCAACGGTTATGGTGCCAAGCTCACTAACATCTTCTCCACGGAGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtcttcattttctccctgaaagtttgtttgtgtcttcgggtttaattgaacagttctagggttttcaagtcctcatttaattggagtatttctcaattga...

Basic information

species Glycine max
transcript GLYMA15G43170.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G43170.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g47150.1 (Oryza sativa), 5'ss of exon 1
CGGCGGACGCAACGGTTATGGTGCCAAGCTCACTAACATCTTCTCCACGGAGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtc---ttcattttctccctgaaagtttgtttgtgtcttcgggtttaattgaacagt----tctagggttttcaagtcctcatttaattggagtatttctcaattga
||||||| | || |||||||| ||||||||||| ||||||||||| |||||||| || || || ||||||||||||   || ||||||||||| || |||||    |||||||  |||   | ||||| |||     | ||  ||| | | |  | |    ||| |||  |     |   | |  || || | | | ||| |     
CGGCGGAAGGAATGGTTATGGCGCCAAGCTCACCAACATCTTCTCGACGGAGTTCGTGATTGAGACCGCCGATGGACGTCGGCAGAAGAAGTACAAGCAGgttaaattcatttgttcctccagagtttttttccccttgcgtattttagttagtactgacatctgggggat--ggattagcttagaaatgaact-tctcttac----

upper sequence: GLYMA15G43170.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G021270_T01 (Zea mays), 5'ss of exon 1
CGGCGGACGCAACGGTTATGGTGCCAAGCTCACTAACATCTTCTCCACGGAGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtcttcattttctccctgaaagtttgtttgtgtcttcgggtttaattgaacagttctagggttttcaagtcctcatttaattggagtatttctcaattga-----------
||||||  | ||||| || || ||||| |||||||||||||||||||| ||||| |||||||| |||||||||||    || ||||||||||| || |||||    | |||     ||   || |  ||| |   ||   || || ||  | ||| ||   ||||    |  | || |     | ||   | |  |||||           
CGGCGGGAGGAACGGATACGGCGCCAAACTCACTAACATCTTCTCCACTGAGTTCGTCATCGAGACCGCCGATGGGCGTCGCCAGAAGAAGTACAAGCAGgtgacaagttt-----tggctgtct-cttgggcgctc---ttcaaatgggc-gttttaccctttt-ggtttgttatatttcctgtgtggatgtgtattgaaatggggtaga

upper sequence: GLYMA15G43170.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0064g00560.t01 (Vitis vinifera), 5'ss of exon 1
CGGCGGACGCAACGGTTATGGTGCCAAGCTCACTAACATCTTCTCCACGGAGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtcttca--ttttctccctgaaagtttgtttgtgtcttcgggtttaattgaacagttctagggttttcaagtcctcatttaattggagtatttctcaattga----
||| ||  | || || || || || |||||||| || || || || ||||||||||| ||||| ||||| ||||| | ||| |||||||||||||| ||||| |  |  | ||    || |   || |   || ||||    ||   |||    ||||| |  |    |  || |  ||    |     |||| | || ||     
CGGTGGGAGGAATGGGTACGGGGCGAAGCTCACGAATATTTTTTCAACGGAGTTTGTGATCGAGACCGCAGATGGGAGGCGCCAGAAGAAGTATAAGCAGgtataaaagtatttgggcttaggattagg--gtttctttattttcttttg----gttcttgaatgaggagttcttttttcgggttttacatttttgaactgtaatt

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|193391975|gb|FK355656.1|FK355656
EST:     AGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAG                         GTGTTCTCCAACAACATGGGGAAGAAGTCTGAGCCAGTGATAACCAAATGC
genomic: AGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtcttcattt ... tggttgaaagGTGTTCTCCAACAACATGGGGAAGAAGTCTGAGCCAGTGATAACCAAATGC
EST: gi|208182248|gb|GD980261.1|GD980261
EST:     AGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAG                         GTGTTCTCCAACAACATGGGGAAGAAGTCTGAGCCAG
genomic: AGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtcttcattt ... tggttgaaagGTGTTCTCCAACAACATGGGGAAGAAGTCTGAGCCAG
EST: gi|193511738|gb|FK469917.1|FK469917
EST:     AGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAG                         GTGTTCTCCAACAACATGGGGAAGAAGTCTGAGCCAGTGATAACCAAATGC
genomic: AGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtcttcattt ... tggttgaaagGTGTTCTCCAACAACATGGGGAAGAAGTCTGAGCCAGTGATAACCAAATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCGGACGCAACGGTTATGGTGCCAAGCTCACTAACATCTTCTCCACGGAGTTTGTCATCGAAACCGCCGATGGAAAGCGTCAGAAGAAGTATAAACAGgtcttcattttctccctgaaagtttgtttgtgtcttcgggtttaattgaacagttctagggttttcaagtcctcatttaattggagtatttctcaattga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctccc