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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGGTGTCTACTAATTGAGCCATTTCCAGAATCAGCTCTAAATGAACAGGCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagcccagatgatattatcgatgctgtcaattagtttcttgtacggaattgtaatgcgaaacagagtggttactaagattacttgtgttctgaa...

Basic information

species Glycine max
transcript GLYMA19G21400.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os06g45000.2 (Oryza sativa), 5'ss of exon 6
TTAGGTGTCTACTAATTGAGCCATTTCCAGAATCAGCTCTAAATGAACAGGCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagtt---agcccagatgatatta----tcgat----gct------gtcaattagtttcttgtacgga-----attgtaatgcgaaacagagt---ggttactaagattacttgtg-ttctgaa-------------------------------------
| || || || || || || |||||||| ||||| || || ||||| || ||||||||| || ||||||| || ||||||||||||||  | ||||| |||| ||||   |||   | | |||| |    | |||    |||      |||||  | |  | | |  |||     | ||||    |  |    ||     || ||||  || | ||||  |||| |                                     
TGAGATGCCTTCTGATAGAACCATTTCCTGAATCTGCCCTTAATGAGCAAGCTGGGAAATTGTTGCTTGAGAACTATGAGGAGTATGCACGGCATGCAAGgtcagtttttagcgttg-taatatcaaaccttgattagagctctactggtcaaagaatgccatattaggattgccactgtagcatgctatgttgtttcacttgctaaagtttcatgtggctctgtaattagttactgattatttcatgttgcttcatatccag

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G153924_T01 (Zea mays), 5'ss of exon 6
TTAGGTGTCTACTAATTGAGCCATTTCCAGAATCAGCTCTAAATGAACAGGCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagcccaga-tgatattatcga-------tgctgtcaattagtttcttgtacggaattg--taatgc--gaaaca--gagtggttacta--------agattacttgtgttctgaa---------------------------------------
| || || || || ||||| |||||||| ||||| || || |||||||| ||||||||  || | ||||||||||||||||| |||||  ||||||| |||| ||    |   || | | ||||  ||       ||||   |  ||   |||| |  |  |||   || |||  |||| |   ||   ||| |         |||| |    |||| |  |                                       
TGAGATGCCTTCTGATTGAACCATTTCCTGAATCTGCACTTAATGAACAAGCTGGGAAGATGTTACTTGAAAATTATGAGGAATATGCACGACATGCAAGgtcagcc--cttggacttacattagtgacttggattgctcagagatatcctctttttggtcattatttattgccagaaatactcagcaattatttgacaaagcagatcataattgttttataggtatgttgctgatggttccattgtgctccataatgcag

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G895435_T01 (Zea mays), 5'ss of exon 6
TTAGGTGTCTACTAATTGAGCCATTTCCAGAATCAGCTCTAAATGAACAGGCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagtt----agcccagatgat--attatcgatgctgtcaattagtttcttgt------acggaattgtaatgcgaaac--agagtggtta--ctaagattacttgtgttctgaa-----------------------
| || || || ||  | || |||||||| ||||| || || |||||||| ||||||||  |||| || |||||||||||||| |||||  | ||||| |||| ||      | |  | || ||  | |     ||||   |  |    |||| |      |  | | ||||    ||| |   || |  |||  | |  | ||||     |                            
TGAGATGCCTTCTGGTCGAACCATTTCCTGAATCTGCACTTAATGAACAAGCTGGGAAGATGCTACTCGAAAATTATGAGGAATATGCACGGCATGCAAGgtcagcccttgaacttacattatcaacttggagtgctcatacgtgtcctcttattggtgaaaagtactgtatcaggaaccttcgattctttatgccagcaatactgacactacagcaattatgttactccataatgcag

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 5
lower sequence: AT5G05080.2 (Arabidopsis thaliana), 5'ss of exon 6
TTAGGTGTCTACTAATTGAGCCATTTCCAGAATCAGCTCTAAATGAACAGGCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagcccagatgatattatcgatgctgtcaattagtttcttgtacggaattgtaatgcgaaacagagtggttac-taagattacttgtgttctgaa
| |||||  || |||| ||||||||||||||||| ||  |||||||||| ||||| ||  |||| |||||||| ||||| |||||||| || ||||| ||||||| || |     || | | |   ||| ||||||    | |||  |      |||   |   | |   | || |||  ||  |||||| || | | |  
TAAGGTGCTTATTAATCGAGCCATTTCCAGAATCTGCATTAAATGAACAAGCTGGCAAGATGCTACTTGAAAACTATGACGAGTATGCGAGGCATGCTAGgtgagctatctactttggtttca--aatgttgtcaaaccttctctactttttcgttgc--taaaagatgaaatgcttatatactattact-gtatgcag--

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 5
lower sequence: Vv08s0040g00460.t01 (Vitis vinifera), 5'ss of exon 7
TTAGGTGTCTACTAATTGAGCCATTTCCAGAATCAGCTCTAAATGAACAGGCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagcccagatgatattatc--gatgctgtcaattagtttcttgtacggaattgtaatgcgaaa--cagagtggttactaagattacttgtgttctgaa
| |||||| | || || || |||||||||||||||||  | |||||||||||||| ||  ||||||||||||||||||||||||||||||| ||||| ||||||     ||    | ||||   |   ||| |||   || |   |        |  |   ||| |||   || ||| | ||  |||||     | ||  ||| 
TCAGGTGTTTGCTGATCGAACCATTTCCAGAATCAGCCTTGAATGAACAGGCTGGCAAGATGCTGCTTGAAAATTATGAGGAGTATGCCAGGCATGCAAGgtgatgcctccatctttatatccacctaatgttgtt--ttggaagcacacggaaaccttacatgtgaatatcatagttgatatcaagatagaccg-gtcttga-

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|58019402|gb|CX706144.1|CX706144
EST:     GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAG                         ACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
genomic: GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagc ... tacgctgcagACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
EST: gi|58019541|gb|CX706283.1|CX706283
EST:     GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAG                         ACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
genomic: GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagc ... tacgctgcagACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
EST: gi|209727942|gb|BW663456.1|BW663456
EST:     GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAG                         ACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
genomic: GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagc ... tacgctgcagACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
EST: gi|22931116|gb|BU548255.1|BU548255
EST:     GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAG                         ACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
genomic: GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagc ... tacgctgcagACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
EST: gi|58015211|gb|CX701953.1|CX701953
EST:     GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAG                         ACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
genomic: GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagc ... tacgctgcagACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
EST: gi|213611080|gb|DB974982.1|DB974982
EST:     CTGGGAAACTGCTGCTTGAAAATTTA-GAGGAGTATGCCAGACATGCCAG                         ACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACAGTAGC
genomic: CTGGGAAACTGCTGCTTGAAAA-TTATGAGGAGTATGCCAGACATGCCAGgtgagttagc ... tacgctgcagACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
EST: gi|58021744|gb|CX708485.1|CX708485
EST:     GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAG                         ACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC
genomic: GCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagc ... tacgctgcagACTTTACACAGGAATCCATGCAAAACCAAAGTCCAAATTCAAAACTGGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAGGTGTCTACTAATTGAGCCATTTCCAGAATCAGCTCTAAATGAACAGGCTGGGAAACTGCTGCTTGAAAATTATGAGGAGTATGCCAGACATGCCAGgtgagttagcccagatgatattatcgatgctgtcaattagtttcttgtacggaattgtaatgcgaaacagagtggttactaagattacttgtgttctgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG