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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaatcaaattaattttattatatctatgcacaaattatgctaatattaattttataaatttaattaaaatgtactgatgct...

Basic information

species Glycine max
transcript GLYMA20G16100.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 5'ss of exon 3
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaa--tcaaattaattttattatatctatgcacaaattatgctaatattaattttataa-atttaattaaaatgtactgatgct----
||||| || ||||| ||| | || || ||||| ||||| |||||||||||||||||||| || || || || |||||||| ||||||     ||| | |||| |||  ||  || |||   ||| | |     || || || |||   |    || || ||| || |||||||  |||| | | |      
GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGgtac----cat-tgatcttcaacttcccatgaatcagattgttttcgctca-aatttctgcacttccacatgttttaatatgtaattaag-tgtatttaggaattag

upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G860590_T01 (Zea mays), 5'ss of exon 3
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaatcaaattaattttattatatctatgcacaaattatgc-taatattaattttataa--atttaatta--aaatgtactgatgct
|||||||| || ||||||||||| || |||||| | ||||||||||||||||||||||| || || || || |||||||||||||||| |   |||  ||| | |   |   |  |     | |||   ||  ||  |||     |||| ||  | || ||  | || |||   ||| | |   |||  
GCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAGgtatctg--atccaatc-caacagaggatgctcagcctctatgattgtccattttacatgcaatactagctatagaatgacttgattgtcaaaagaaaaaatg--

upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: AC207342.3_FGT008 (Zea mays), 5'ss of exon 3
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaatcaaattaattttattatatctatgcacaaattatgctaatattaattttataaatttaattaa-aatgtactgatgct---
|| || || || || ||  |||| || || || ||||| |||||||||||||||||||| || || || || |||||||| ||||||  || |   |||  |||| ||   ||  |   |||| ||  |    ||   | | ||    |    | |       |     |  ||  |      |    
GCCGCCAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGgta-gta-cgcttcaa-tccagtccccttcttccaatta-atgcagctccagcctctcctctcctctcctctcccgtcatggcggacgatcgatcagctcaacc

upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G42050.1 (Arabidopsis thaliana), 5'ss of exon 2
----------------GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaatcaaattaattttattatatctatgcacaaattatgctaatattaattttataaatttaattaaaatgtactgatgct
                || || || || |||||| | || |||||    |  ||||  || |||||||| || ||||| ||||||||||||||||||||||||  ||  ||    |    | |    |   |||  ||       |||     |     |  ||  || ||| |     |||| |||||  |        
TCATGGAATCTACGAGGCAGCTAGCTTCGGAGGAACAAACATTGAGTTGAATGCTTTTGAAGACAAGAAATGTCCTGGCGAATCTCGTTTCCCTGCTCAGgtac-tactat---gtacttactttcttgcgtttctttgagctcttgcttttgtctaaatgctaacaaattttttggggtaataaaaataaag-------

upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 5'ss of exon 3
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatata-tcatctcatctccaatcaaattaattttattatatctatgcacaaattatgctaatattaattttataaatttaattaaaatgtactgatgct--
|||||||| ||||||||| | || ||||||||||| |||||||||||||||||||||||||| ||||| || |||||||||||||| | |  ||   || |     |||     || | | |  |        || | | || | ||    |||||  |        ||   || |    |||    
GCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAGgtctgttctccaatcttacttgatctgccaaactgtgtagt--tgggctactagtcat-caaaggcaaatttggtttggggtctttgtatatggccatgaatt

upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S6_446V6.1 (Physcomitrella patens), 5'ss of exon 3
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctc-caatcaaattaattttattatatctatgc----acaaattatgctaatattaat---tttataaatttaattaaaatgtactgatgct------------------------------------------------------------------------------------
|||||||| |||||||| ||||| || |||||||| |||||||| |||||||||||||  || |||||  | || ||||| ||||| | |  |  |||||||  | || | |||  |  |    |  | | |       ||  ||||  |  | | ||   ||  |    |   || |||||      |||                                                                                     
GCTGCAAGCTTTGGAGGCTCCAACATAGATCCAACAGCTTGGGAAGACAAGAAGTGCCGCGGAGAATCAAGATTTCCTGCACAGgtttttg-ctcctcatctttctattatattcttactgcagttgcaaagttaggggaaggtatgtcatgaatcatgtcttcttgtggtctcttgaaatgc-tgagtgcctcaacctctccagatggtcgacaatcaccagagtcgcattttgaactgccattggaataatgtttcttcgtgtgtggggatcag

upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 3
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaatcaaattaattttattatatctatgcacaaattatgctaatattaattttataaatttaattaaaatgtactgatgct
||||| |||||||| || || || || ||||| || || ||||| ||||||||||| | ||| |||||||| |||||||| ||||| | | |   ||  | ||  ||    ||  || |      | | ||   |        |||  ||   |   |   |    |  |              
GCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAGgtttgtcttcacttctttctcat----ttgcttctcgagcgtgtgtgaggatccgggcttaactttctctcgctttgtcctctccag-------------

upper sequence: GLYMA20G16100.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ24245 (Selaginella moellendorffii), 5'ss of exon 3
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaatcaaattaattttattatatctatgcacaaattatgctaatattaattttataaatttaattaaaatgtactgatgct
||  ||||||||||||| ||||| || ||| |||| || |||||||||||||||||||  || || ||  | ||||| |||||||| | | ||   || | | | |  | | ||      || |   | | |   |  |     |     ||    | |    |  | |     ||| |     
GCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAGgtttgtctc---tcgttttctaggagaatagaaagctttttcttgttcttgagctgcaagagctacaaaggaaaacccatcgtgatcccatacag-----

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|192309118|gb|FG999065.1|FG999065
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|209722281|gb|BW675075.1|BW675075
EST:     TCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGA-TCCTTT
genomic: TCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCC-TT
EST: gi|14205657|gb|BG839335.1|BG839335
EST:     GGCTTGGGAGGACAAGAGAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: GGCTTGGGAGGACAAGA-AGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|192313456|gb|FK005522.1|FK005522
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|58019242|gb|CX705984.1|CX705984
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|209721490|gb|BW672241.1|BW672241
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|58018944|gb|CX705686.1|CX705686
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|11274562|gb|BF324905.1|BF324905
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAC                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|21602164|gb|BQ612495.1|BQ612495
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|192313455|gb|FK005521.1|FK005521
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|23735151|gb|BU765842.1|BU765842
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
EST: gi|254346210|gb|GR859823.1|GR859823
EST:     CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT
genomic: CGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatcatctcatctccaatcaaattaattttattatatctatgcacaaattatgctaatattaattttataaatttaattaaaatgtactgatgct

- - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT