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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgtttttcatccaattta...

Basic information

species Glycine max
transcript GLYMA18G08220.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv00s0194g00030.t01 (Vitis vinifera), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgt-tgacttgttgcttctgcttgattcgtgacgtatttgtgtt--tttcatccaattta
  |||||||| |||||||||||||| |||||||||||||||||||| |||||   ||||||||| || |||||||||||  ||||||||||  |||| ||||| |||||         | |||| ||  ||||   |||      | |||     ||| | || |       |  | | || ||  |  |   || | |||  
-ATTCCAGGCGGAGATCAACCAGCTGCTCAGTCTCATCATCAACACTTTCTATAGCAACAAGGAGATTTTCCTTCGTGAGATCATCAGCAATTCCTCCGATgtgagttttcagaacagtttctccttcacttctccttttaaggatctgatcgactgcgtgtgttgcgcgtatttcatgttcgtaatgatgcaatgcgatt--

upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv19s0015g01090.t01 (Vitis vinifera), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgc--ttctgcttgattcgtgacgtatttgtgtttt-tcatccaattta
 ||||||||||||||||||||| ||| | ||| | ||||||||||||||||||  ||||||||| || || || ||||| |||||||||||  ||||||||||||||    |  || || ||| ||||  | |   |||     |||   || | ||  | ||| || ||| | | |  || |||  | | |      |||  
-TTTCCAGGCTGAGATCAACCAACTCTTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTTCTCCGTGAGCTCATCAGCAATTCCTCTGATgtaagtcctatactttttatctttttttttcctcatttaatcagtttttttttcgcgatcctgttttatttgcggctgatctgttctctgttggtttatt--

upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgtttttc--atccaattta-
  |||||||| |||||||||||| | || ||| | || |||||||| ||||||  |||||||||||| ||| |  | ||  | ||||| ||| | || ||||||| ||||||    ||| |     ||| |   | |||   || ||  ||   |   |||    |  |||    |   ||    | |    || | |   | 
-CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatcatt--ctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat

upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S258_52V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgt---ttttcatccaattta
  || ||||| || ||||| ||| | || ||| | ||||||||||||||||||  ||||||||| || ||||| || ||||| ||||||||  | ||||||||||||    | || ||        | || | |  | |   |    |  |||| |   |   |  ||  ||| | | |    |    || |       |  |
-CTTTCAGGCGGAAATCAATCAGTTGCTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTGCGAGAACTTATCAGCAATTCTTCTGATgtaagtgc--tagtgctgacgaaagtcccatgcggtcttcttgtcgggattgtagtggccagtctatctgtgtcatgtgcacgccgattcttggttggtgca

upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ25533 (Selaginella moellendorffii), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagt-ttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttg--attcgtgac--gtatttgtgtttttcatccaattta---
  |||||||| |||||||||||||| |||||||||||||||||||||||||||  ||||||||| |||||| | || || ||||||||||| ||||| ||||| ||| ||    | || |    |  |   || ||  |  |||| | ||  | |  |||||   ||  |||  | ||   | ||||  || ||  | | ||||    
-CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatattttactgctattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcattctttctgcgatttccag

upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ29061 (Selaginella moellendorffii), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgtttttcatccaattta
  ||||||||||||||||||||||| |||||||||||||||||||| ||||||  ||||||||| || ||| | || || ||||||||||| ||||| ||||| |||       ||   |   ||| | |||||  |   ||| ||  |  | || ||||| ||      | | ||    ||||  |             
-GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagt------atttcgcctccttgttcttccagt---tcttgtcaaactctttcttcttctcatgctgcgccgc---tgtgactccag---------

upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ22362 (Selaginella moellendorffii), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagt-ttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttg--attcgtgac--gtatttgtgtttttcatccaattta---
  |||||||| |||||||||||||| |||||||||||||||||||||||||||  ||||||||| |||||| | || || ||||||||||| ||||| ||||| ||| ||    | || |    |  |   |  ||     |||| | ||  | |  |||||   ||  |||  | ||   | |||| ||| ||  | | ||||    
-CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatatttcactgcgattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcgttctttctgcgatttccag

upper sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcct---ttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgtttttcatccaattta
  ||||||||||||||||||||||| |||||||||||||||||||| ||||||  ||||||||| || ||| | || || ||||||||||| ||||| ||||| ||| | |    || |   ||   | |||       | | |||  ||  | || |||       ||| ||  |                           
-GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag---------------------------

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|193535132|gb|FK489478.1|FK489478
EST:     TACTCCAACAAGGAAATCTTCCTTCGCGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|13181413|gb|BG352683.1|BG352683
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|151402250|gb|EV272063.1|EV272063
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|13125720|gb|BG316290.1|BG316290
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|298180770|gb|HO022209.1|HO022209
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|10846004|gb|BF068997.1|BF068997
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|298189867|gb|HO038270.1|HO038270
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|10845994|gb|BF068991.1|BF068991
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|193309837|gb|FK274545.1|FK274545
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCACCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|57574579|gb|CX547554.1|CX547554
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|7685027|gb|AW755675.1|AW755675
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|208058461|gb|GD856924.1|GD856924
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|192297125|gb|FG988221.1|FG988221
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|16996959|gb|BM086331.1|BM086331
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|208285234|gb|GE089086.1|GE089086
EST:     CCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: CCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
EST: gi|9987183|gb|BE661291.1|BE661291
EST:     TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGA                         TGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA
genomic: TACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttc ... taaaattgtaGGCTTTGGACAAGATTAGATTTGAGAGTTTGACGGACAAGAGCAAGCTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgtttttcatccaattta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttcct