Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttttgctggactctgttacctctaatacggttgttaggaaataaatatgtaatatttgttctaaagatagctatttattttgcttgtatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG

Basic information

species Glycine max
transcript GLYMA18G08230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 2
--------------------------------tttgttttgctggactctgttacctctaatacggt-tgttaggaaataaatatgtaatatttgttctaaagatagctatttattttgcttgtat-atgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG
                                   ||  | ||     || ||    || |  | || |  | ||    |  |   |  | | |||  |   | | |  ||||  |   ||||| |  ||||||||| || |||||  | || || || |||||||||||||| ||||| ||||||||||| || || || ||| ||||||||||| 
gtaagtccgccgcattcgccattggttggggcgccgtactcctccttccttttgttgctgagcctgtctcattgggggaatttgactggtgtgtgtggttgggttgg--attttgtggccttgtgttgtgcagTCAGCGTGAGCGAGGTCGAGGCGCTGTACGAGCTCTTCAAGAAGATAAGCAGTGCTGTGATTGATGACGGGCTGATTAACAAG-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 2
---------------tttgttttgctggactctgttacctctaatacggttgtt--aggaaataaat--------atgtaatatttgttctaa-------agatagct--atttattttgcttgtatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG
               ||  | |  |||| | ||| | | | |   |||   |    | ||| | |||          |   | || | |||         ||   |||     | |  |  ||||   ||||||||| || |||||  | || || || |||||||| ||||| ||||| ||||||||||| ||||| |||||| ||||||||||| 
gtaagcatgatctgcttcctctccctggtcgctgcttcatttcgcacgcacggggaatgaattgaattgacgcctgcgccttgttcggtctgggtggctgagtgggctttgcctgtgcttgttgttcctgcagTCAGCGTGAGCGAGGTCGAGGCTCTGTACGAGCTGTTCAAGAAGATAAGCAGTGCTGTCATCGATGATGGGCTGATTAACAAG-
















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|151397479|gb|EV267352.1|EV267352
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|38192551|gb|CF921757.1|CF921757
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|38193812|gb|CF923018.1|CF923018
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|16349164|gb|BI974759.1|BI974759
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|192298955|gb|FG987700.1|FG987700
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|18848425|gb|BM567661.1|BM567661
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGTGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|8284959|gb|BE022518.1|BE022518
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|8283189|gb|BE020750.1|BE020750
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|192334402|gb|FK025551.1|FK025551
EST:     CAGCCAAGAGGTCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|209718662|gb|BW674764.1|BW674764
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|254347752|gb|GR854001.1|GR854001
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|192320225|gb|FK014239.1|FK014239
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|213592918|gb|DB966023.1|DB966023
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|254324275|gb|GR840592.1|GR840592
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
EST: gi|308098080|gb|HO761251.1|HO761251
EST:     CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTT                         CAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG
genomic: CAGCCAAGAGGCCTTGAAGATCCTGAACTTCTTGCTAGAGAGACTGTGTGtatgcactta ... tatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatatgtaatatttgttctaaagatagctatttattttgcttgtatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG
                 ttctaaa  putative branch site (score: 2)
        taatatttgttctaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttttgctggactctgttacctctaatacggttgttaggaaataaatatgtaatatttgttctaaagatagctatttattttgcttgtatatgcagtCAGTGTAAGCGAAATAGAAGCACTTTACGAGCTCTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG

- - - -tgctgga
- - - - - - - - -tgttacc
- - - - - - - - - - - - - - - - ggttgtt
- - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcttg