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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagccatgtgtgagcgttgacgttttctttattcttttgtgaagttttggattttgttcttatgtcttggttgggtttactttttcgattcgagtt...

Basic information

species Glycine max
transcript GLYMA17G17520.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G154799_T01 (Zea mays), 5'ss of exon 2
GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGaaggtgagagccatgtgtgagcgttgacgttttctttattcttttgtgaagttttggat-----tttgttcttatgtcttggttgggtttactttttcgattcgagtt
|||||| |||||||| ||||| ||||||||||||||  | |    |     || ||||| ||| ||||||||||||||||| |||||||||||||||||||| ||       | |        | | | | ||       |||| |  |||  |         | | |  |||   |  |     | || |    |    |  ||
GGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCCGGGCCGGGAGCGATGAGAGATGCGTCATTAAGATCCTGAAGCCCGTGAAGAAGAAGaaggtcagctttgctttta-----caatgctctgttgcggtggttgtcacatttctggcaaccagctatacggatggaatcataaatatgacatacagggactgcctt

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G138774_T01 (Zea mays), 5'ss of exon 3
---GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGaaggtgagagccatgtgtgagcgttgacgttttctttatt-cttttgtgaagttttggattttgttcttatgtcttggttgggtttactttttcgattcgagtt
   |||||| |||||||| ||||| ||||||||||||||  | |    |     || ||| | ||| ||||||||||||||||| |||||||||||||||         ||  |      ||  ||  |   |  || |  | ||| ||       |   |  |     |||   |  |     | ||      |    |  ||
GAAGGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCCGGGTCGGGAGCGATGAAAGATGCGTCATTAAGATCCTGAAGCCCGTGAAGAAGAAGgtcaactttgcttttacaatgctctgttgcggtggttgtcacatttctggcaaccagcgctacgg----atggaatcataaatctgacacacagggactgcctt

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 2
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 5'ss of exon 2
GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGaaggtgag-agccatgtgtgagcgttgacgttt-tctttattcttttgtgaa-gttttggattttgttcttatgtcttggttgggtttactttttcg---attcgagtt-------------
||| || ||||| |||||||||||||| || |||||  ||||    || ||    ||||||||||| || |||||  |||| || |||||||||||||||||||| ||  |     |   | |    ||| |||  ||| |  |  ||| |   ||  |||    |   |  ||||||| |  ||| | | |     |||    ||             
GGTAGGAAGGGGAAAATACAGTGAGGTCTTTGAAGGCATTCATGCTACTGATAACGAGAAATGTGTTATCAAGATTTTGAAGCCTGTGAAGAAGAAGaaggtgagtagatacagccgcttgcttgtttttatctcaattgtgctcagaatgaagtgtgtttctggcccttcacttggtttgaattattctctaacatattttgcttctccttgacgcag

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 2
GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGaaggtgagagccatgtgtgagcgttgacgttttctttattcttttgtgaagttttggattttgttcttatgtcttggttg--ggtttactttttcgattcgagtt------
||| || ||||||||||||||||| |||||||| || || ||||||||||||  |||||| ||| | |||||||| || ||||||||||| ||||| ||||||||  ||   | |     |||||      |  |   | |||  || || |  |||        || ||||| |||  |||||  |||  |  || ||| |      
GGTTGGGAGGGGGAAATACAGTGAAGTGTTCGAGGGCGTGCACTGCACCGACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccctctttta--tattgac-----ttgcagcttcttggaaatttatttattccaccagaatttcttgtttgttggtttg-tttaacattttgagcttttcga

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGaaggtgagagccatgtgtgagcgttgacgttttctttattcttttgtgaagttttggattttgttcttatgtcttggttgggtttactttttcgattcgagtt-
 || ||  ||||||||||||||||||| || ||||||||||||  |    || |||||   || || ||||||||  |||| || |||||||| || |||||   |  | |  ||   |       ||    | || | ||| || |   |||          |  | | | | ||      | ||| | |       || 
AGTAGGGCGGGGGAAATACAGTGAGGTTTTTGAAGGTGTTCACGCCGTGAACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagcttcggtacccaacattcttcatctgatgcattt-tgcatccttgatagagccagtcgtttatggttttccagcaatttcttgggcaagcttt

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|15203622|gb|BI426390.1|BI426390
EST:     CGGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc
EST: gi|9564123|gb|BE473632.1|BE473632
EST:     CGGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc
EST: gi|13478623|gb|BG508028.1|BG508028
EST:     CTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc
EST: gi|207738098|gb|GD715106.1|GD715106
EST:     CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc
EST: gi|18038926|gb|BM307220.1|BM307220
EST:     CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc
EST: gi|22522067|gb|BU080878.1|BU080878
EST:     CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc
EST: gi|9565463|gb|BE474972.1|BE474972
EST:     CGGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc
EST: gi|254330876|gb|GR842141.1|GR842141
EST:     CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAG                       
genomic: CCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagcca ... ctgaatgc

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGAAGgtgagagccatgtgtgagcgttgacgttttctttattcttttgtgaagttttggattttgttcttatgtcttggttgggtttactttttcgattcgagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG