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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgttattataaccaatgggatatattccttaattaattaatgcacttgcctatataatgtag

Basic information

species Glycine max
transcript GLYMA03G27660.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01140.t01 (Vitis vinifera), 5'ss of exon 4
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgt-acgtgtgtgtgttattataaccaatgggatatattccttaattaattaatgcacttgcctatataatgtag------------------------------
|||||||||||| ||||||||| |||| ||| ||||||||||||| ||||| ||| | || |||||  ||||| |  | |||||||||||    |||||||| |  |       || || |      | |  | | ||   || || |   ||  || | | |  | | |                                  
TGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTCCCGGATTATATATGGATGGCAGAAGATGGAATTAAGATGCAGgttagatccaaaaatttttct--tttttagagtttgttttgtatttga--gattgaccttcattcaaagtcctaactttgataattttcattgagatatgcgga

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 5'ss of exon 8
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgtt--atta-taaccaatgggata--tattccttaattaattaatg--cacttgcctatataatgtag----------------------------------------------------------------------------------
| | |||||||| ||||||||||| || |||  |||||||||||| ||||| ||| ||||||||||  ||||||||   |||||||||||    ||||||||  |       |||  || | ||| |      | |  | |     || ||  ||||   || |   || | |  |  |                                                                                   
TTCATGTTGGGTTGAAGATCCAAACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATGGAATAAAGATGCAGgtcagaaaacaagttcaatcactaatctcccaaacagttgtagaaaaaatagataatatccagtcatctttttcttaaaatttttcaagtacgcaattggtttgaagctatgcttttgtccctttcctgcctaattggttttgaaattgtcgattgttgcag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 5'ss of exon 8
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgttattataaccaatgggat-----atattcctt----aattaattaatgc--acttgcctatataatgtag----------------------------------------------------------------------------------
  | |||||||| |||||||||||||| |||  |||||||||||| ||||| ||| | |||||||   |||||||| | |||||||||||    ||||||||  |       |||| |  || || |    |     | | |  |     |||||  ||||    | |   || | |  |  |                                                                                   
CACATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTTTATATGGGTTGCAGAAGATGGAATAAAGATGCAGgtcagaagacaagttaattcaatcactaatctcccaaacagttgtaggaaaattagataatatctattcatctttttcttaaaatatttcaagtgtgcaactggtttgaagctatgcttttatcctctcctgcctaaattggttttgaaattgtcgattgttgtag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 5'ss of exon 6
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgttattataaccaatgggat-----atattcctt----aattaattaatgc--acttgcctatataatgtag--------------------------------------------------------------------------------
  | |||||||| |||||||||||||| |||  |||||||||||| ||||| ||| | ||||||||  |||||||| | |||||||||||    ||||||||| |       |||| |  || || |    |     | | |  |     |||||  ||||      |   || | |  |  |                                                                                 
CTCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATGGAATAAAGATGCAGgtaagaagacaagttaattcaatcactaatctcccaaacagttgtaggaaaattagataatatctgttgatctttttcttaaaattttttaggtatgcaactggtttgaagctgcttttatccctttcctgcctaattggttttgaaattgtcgattattgcag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01210.t01 (Vitis vinifera), 5'ss of exon 8
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgttattataaccaatgggatatattccttaattaattaatgcacttgcctatataatgtag--------------------
|||||||||||| ||||||||| |||| ||| ||||||||||||| ||||| ||| | ||||||||  ||||| || | |||||||||||    ||||||||  |      |  | || |   |    | || ||||   || || |  | || || |    ||  ||||| |                    
TGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTGCCAGATTATATATGGATTGCAGAAGATGGAATTAAGATGCAGgttagatccaataattttttcctcttcagaatttattttgtatttgac-attgaacat---cattcaatgtcgattttcattgagatatgcag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 5'ss of exon 1
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgttattataaccaatgggat-----atattcctt----aattaattaatgc--acttgcctatataatgtag----------------------------------------------------------------------------------
  | |||||||| |||||||||||||| |||  |||||||||||| ||||| ||| |   |||||   |||||||| | |||||||||||    ||||||||  |       |||| |  || |  |    |     | | |  |     |||||  ||||    | |   || | |  |  |                                                                                   
CACATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCAAAGATTTTATATGGGTTGCAGAAGATGGAATAAAGATGCAGgtcagaagacaagttaattcaatccctaatctcccaaacagttgtaggaaaattagataatatctattcatctttttcttaaaatatttcacgtgtgcaactggtttgaagctatgcttttatcctctcctgcctaaattggttttgaaattgtcgattgttgtag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 5'ss of exon 4
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgtt--atta-taaccaatgggatatattccttaa--ttaattaatgc--acttgcctatataatgtag--------------------------------------------------------------------------------
||| ||||||||  ||||||||||||| |||  |||||||||||||||||| ||| | ||| ||||  |||||||| | |||||||||||    ||||||||  |       |||  || | ||| |      |||  ||    ||  |||   |||      |   || | |  |  |                                                                                 
TGCATGTTGGGTTAAAGATCCAAATGGGGATTATTTCAAGAAGCATCTTGCTAGGATCCCATATTATATATGGGTTACAGAAGATGGAATAAAGATGCAGgtcagaagacaagttcaatcactaatctcccaaataattttaggaaaattagacaatatctgttaatctttttcttaaaatttttcaagtatgcaactggtttgaagttgcttttatccctttcctgcctaattggttttgaaattgtcgattattgcag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 5'ss of exon 12
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgtt--atta-taaccaatgggatatattccttaattaattaatgc--acttgcctatataatgtag------------------------------------------------------------------------------------------------------
| | |||||||| ||||||||| | || |||  |||||||||||| ||||| ||| ||||||||||  ||||||||   |||||||||||    ||||||||  |   |   |||  || | ||| |      | |  ||    ||  ||||| |    | ||   ||| || | ||                                                                                                       
TTCATGTTGGGTTGAAGATCCAGACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATGGAATAAAGATGCAGgtcagaaagcaagttcaatcactaatctccccaaca-gttgtagaaaaaattagtatctatttatttatttattttaacattaagtttgattgaagattttctgttaagcaactggtttaaagtaatgcatttagccctttcctgcctaattggttttgaaattgctgattgaaatgtag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 5'ss of exon 8
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgtt--atta-taaccaatgggatatattccttaattaattaatgcacttgcctatataatgtag--------------------------------
| | |||||||| ||||||||||| ||  ||  |||||||||||| ||||| ||| ||||||||||  ||||||||   |||||||||||    ||||||||  |       |||  || | ||| |      | |  ||    ||  || ||||||  ||  |  | |  ||                                   
TTCATGTTGGGTTGAAGATCCAAACGGGAATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATGGAATAAAGATGCAGgtcagaaaacaagttcaatcactaatctccccaaca-gttatagaaaaaagtaatgcctttagccctttcctgcctaattggttttgaaattgctgattgaaatgtag

upper sequence: GLYMA03G27660.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 5'ss of exon 8
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgtt--atta-taaccaatgggata--tattccttaattaattaat--gcacttgcctatataatgtag--------------------------------------------------------------------------------
 || |||||||| |||||||||||||| |||  |||||||||||| ||||| ||| | ||||||||  |||||||| | |||||||||||    ||||||||  |       |||  || | ||| |      | |  | |     |||||  ||||  |   |   || | |  |  |                                                                                 
CGCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATGGAATAAAGATGCAGgtcagaagacaagttcaatcactaatctcctaaacagttgtaggaaaattagataatatgtgttgatctttttcttaaaatttttcaagtatgcaaatggtttgaagctgcttttatccctttcctgcctaattggttttgaaattgtcgattattgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTGTTGGGTGGAAGATCCAAATGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTTCCAGATTACTTATGGGTTTCTGAAGATGGAATGGCCATGCAGgtacgtgtgtgtgttattataaccaatgggatatattccttaattaattaatgcacttgcctatataatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA