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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgctctctaatgggttttatgagctttaaatcattgatgtcaatttgaattgttctaacag

Basic information

species Glycine max
transcript GLYMA03G33270.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33270.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g17710.1 (Oryza sativa), 5'ss of exon 5
CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgctctctaatgggttttatgagctttaaatcattgatgtcaatttgaattgttctaacag
|  |||| ||||| || || || ||||||||||| |||||||||||||| ||||||||||| |||||||  |||||  | |||||||| | |||  | |||||     | ||    ||    |  |   ||   ||     | || ||| |     | || |    |  |||     | | ||  | |  |  |   |  |   |||  |            
CAAGAGACTGCAAGGCTGGTGACTGGAAGAACAAATGTTACCGTTGTGGAGAAAGAGGTCACATAGAAAGAAACTGCCAAAACAGTCCAAGAAATCTCAGgtattgattgataccgttggtcagat---acactgtagcactctgttctaa-----ggtactatgtttgaatta--ctcaagacttctccaatacgtacttggttttccag-----------

upper sequence: GLYMA03G33270.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g02880.1 (Oryza sativa), 5'ss of exon 5
CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgta---ggccataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgctctctaatgggttttatgagctttaaatcattgatgtcaatttgaattgttctaacag
|  |||| ||||| || || || ||||||||||| |||||||| |||||||| |||||||| |||||||  |||||| | ||||| || | |||  | |||||       ||||  | || |   ||     | | | ||   | ||| ||  |     | || ||   |  |||   ||   | || |||    |    |||   | ||   || || | |   
CAAGAGACTGCAAGGCTGGTGACTGGAAGAACAAATGTTACCGCTGTGGGGAGAGAGGTCACATAGAAAGAAACTGTCAAAACAGCCCAAGAAATCTCAGgtattgattgataagttgatctgataaagagcagcacttgc--aattgttccga-----ggtactgtatttgaataatttaacttagattt----ctccaatgcatacttctttttttttcag--

upper sequence: GLYMA03G33270.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 5
CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgctctctaatgggttttat--gagctttaaatcattgatgtcaatt--tgaattgttctaacag
|  |||| ||  | || || || ||||||||||| || ||||||||||| ||||| || ||||||||||  || ||  |||||||||| |  ||  | |||| |   ||  |  |   |   | || | |   |      || ||      || |    | |    |||| ||  | | ||   |   ||  || |  || ||   ||  | |||   | ||    
CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgt-gtttattgttaacactatcagctac-attccacagctatatgacac--acttaagcactatattctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag---

upper sequence: GLYMA03G33270.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 5'ss of exon 3
CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggcc------ataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgc-tctctaatgggttttatga----gctttaaatcattgatgtcaatttgaa-ttgttctaacag-------
| |||||||||||||| || || |||||||| |||||||| || ||||| |||||||||||||| ||||  |||||  ||||||||||||  ||| | |||||  |        | ||   ||  | |||| | |  ||| || ||  |||   ||    |   ||||   | | |  |  |  | ||       || |  |   ||  ||| |  || ||  | || |   |        
CTCGAGATTGCAAAGCTGGAGACTGGAAGAATAAGTGTTATCGGTGTGGAGAAAGAGGTCATATTGAAAGAAACTGCCAGAACAGTCCCAGGAAGCTCAGgtattctcatatggtgattacatgccaaaacatttctctcctgctgccttgacatttttttccatattatatttttgttaagcatgatactgttactgtgcaaagtttttgttagcttaaaactattatgttatattgcag

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|254332769|gb|GR846600.1|GR846600
EST:     AACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: AACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|193696875|gb|FK638017.1|FK638017
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|208156572|gb|GD956854.1|GD956854
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|298199246|gb|HO042609.1|HO042609
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|193684971|gb|FK626495.1|FK626495
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|193455254|gb|FK419693.1|FK419693
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|254344581|gb|GR855452.1|GR855452
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|208318139|gb|GE114078.1|GE114078
EST:     AAAGAGGTCATATAGAAAAGAACTGTAAGAACTAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: AAAGAGGTCATATAGAAAAGAACTGTAAGAAC-AGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|207839844|gb|GD810037.1|GD810037
EST:     -AAGAGGTCAGTATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: AAAGAGGTCA-TATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|19347351|gb|BM892231.1|BM892231
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAAACG-GGACGGAGTCTTTTC-CGTTCAACAGTAAGGTCACGTTCTCCT
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAA-CGTGGACGGAGTCTTT-CACGTTCACCAGTAAGGTCACGTTCTCCT
EST: gi|207765392|gb|GD738171.1|GD738171
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|208022923|gb|GD820933.1|GD820933
EST:     AAAGAGGTCATATAAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: AAAGAGGTCATAT-AGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|254344582|gb|GR855453.1|GR855453
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|208276808|gb|GE073395.1|GE073395
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|7692938|gb|AW761037.1|AW761037
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|193626318|gb|FK572682.1|FK572682
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|208233570|gb|GE031451.1|GE031451
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG
EST: gi|193320057|gb|FK284318.1|FK284318
EST:     GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAG                         CCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCTTCG
genomic: GAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccata ... gttctaacagCCAACGTGGACGGAGTCTTTCACGTTCACCAGTAAGGTCACGTTCTCCTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgctctctaatgggttttatgagctttaaatcattgatgtcaatttgaattgttctaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC