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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAAGGCTAAATCTTTTTGAACAGACGAAGGAAAAACGCAGTGATTAAGCGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGCGGTCGAGATCgtaagtcatgttcaatttctcgctatttcccaaaatttctctttctctctcttttgggtattgaatcgtttcggaatttgtcaaattgaaactagcaatt...

Basic information

species Glycine max
transcript GLYMA01G06270.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G06270.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G52220.1 (Arabidopsis thaliana), 5'ss of exon 1
CGAAAGGCTAAATCTTTTTGAACAGACGAAGGAAAAACGCAGTGA--TTAAGCGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGCGGTCGAGATCgtaagtcatgtt-caatt---tctcgctatttcccaaaatttctctttctctctcttttgggtattgaatcgtttcggaatttgtcaaattgaaactagcaatt--
  ||   ||   | ||      | || |||  |  || |  |  |  || || |     |||||||||||||| || || || ||||| || ||||||||||||||||    ||  ||||   | | | | || |    |||| |    ||   ||   |    |  | ||  |||  ||    | |  | |   | | | |  ||  
--AAGTTCTGGCTTTTAGCCTCCTGAGGAAAAATCAAGGTTGCAACTTTCAGGGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATCgtaagtttcattataattcgttttggattttgcttctaattacaagatc---ctacataaaattctcaactgttagggttcctatgtatt---atccaacgttttc

upper sequence: GLYMA01G06270.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0101g00090.t01 (Vitis vinifera), 5'ss of exon 1
-CGAAAGGCTAAATCTTT--TTGAACAGACGAAGGAAAAACGCAGTGATTAAGCGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGCGGTCGAGATCgtaagtcatgttcaatttctcgctatttcccaaaatttctc----tttctctctcttttgggtattgaat-cgtttcggaatttgtcaaattgaaactagcaatt
  ||||  |  ||  |||  || | || |||||| | |     |   |  || |    | ||||||||||| || |||||||||||||| || || |||||||||||    | |||  || ||   | ||| |   | |||       |||||     ||||     |  | | | | ||  |     ||   || |  ||       
TAGAAAAACGGAAATTTTCATTCACCAAACGAAGCAGAGG---ATAAAAGAAACTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctcttctcttccttttttttttctctacttttctagggtttctgcactttttaaacctcaactacctctctaatccaatcttcttcattcttc-----
















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|193312411|gb|FK276139.1|FK276139
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|193356756|gb|FK318860.1|FK318860
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|208067670|gb|GD866080.1|GD866080
EST:     CGGTCGGGATC                         AATTTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTT
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAA-TTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTT
EST: gi|207687730|gb|GD668527.1|GD668527
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTACCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|193448027|gb|FK411464.1|FK411464
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|208298032|gb|GE093247.1|GE093247
EST:     GGCGGTCGAGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: GGCGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|193308195|gb|FK274862.1|FK274862
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCACAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|208137739|gb|GD938403.1|GD938403
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|208176200|gb|GD973885.1|GD973885
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|193367185|gb|FK329869.1|FK329869
EST:     CGGTCGGGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|298190449|gb|HO032570.1|HO032570
EST:     CGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGCGGCGGTCGAGATC                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGCGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
EST: gi|193587540|gb|FK542575.1|FK542575
EST:     CGGTCGGGATT                         AATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG
genomic: CGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAAGGCTAAATCTTTTTGAACAGACGAAGGAAAAACGCAGTGATTAAGCGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGCGGTCGAGATCgtaagtcatgttcaatttctcgctatttcccaaaatttctctttctctctcttttgggtattgaatcgtttcggaatttgtcaaattgaaactagcaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc