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'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagtacatttgattatattgtaaatgttcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA

Basic information

species Glycine max
transcript GLYMA09G30910.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g49600.2 (Oryza sativa), 3'ss of exon 2
gaagtacatttgattatat-tgtaaatgttcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
 || | |  |  | |||   |||  | | || |     |||     | |||  | ||  |     || |          | |  | ||  |  |   |||||||||| |  ||||||||   ||  |||||||||||||||||||||| |||||||| |||||||| || || ||| 
-aaatgctctaaaatatgcgtgtccaaggtctt---acattacatgtaagtgtttccattctccattatctaaaaaaaaagtgta-tccattctggaacaggaagATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g49600.3 (Oryza sativa), 3'ss of exon 2
gaagtacatttgat-tatattgtaaatgttca---ttatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
    |  |  || | || | | |   ||| ||   |  |  |||     | |||  | ||  |     || |          | |  | ||  |  |   |||||||||| |  ||||||||   ||  |||||||||||||||||||||| |||||||| |||||||| || || ||| 
---ctgtaaatgctctaaaatatgcgtgtccaaggtcttacattacatgtaagtgtttccattctccattatctaaaaaaaaagtgta-tccattctggaacagGAAGATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 3'ss of exon 2
gaagtacatttgattatattgtaaatgttcattatgtattg--tgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
  |||  | || || | ||  | ||| |        |  |   || ||   || |   |||    |    |   | ||   ||   ||   |  |   |||||||||| | |||||| ||   ||||||||||| ||||| || ||||| |||||||||||||| || ||||| ||  
-gagtcaagttaatca-ataatgaatttcggcagcttgataattgcttactttttttttctgaaagaagataattacttacattgtcttcttgctagcacagGAAGATGTTGATCTCTTGAAAAGCCTGAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 2
---gaagtacatttgattatattgtaaatgttcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttg-acagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
    | | |||    ||   |   | |   || || ||  |||  ||   | | ||  || ||  | ||  |||    | |  |   || | |   ||| |||||||||| | |||||||||   ||||| ||||||||||| |||||||| |||||||| |||||||| || || ||| 
tgaaacgaacaaaacatctcacgctgagaattaataattcatttaga--aattagtaactatttcttttagtctgaatttggctt--ctttatcccttgtacagGAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G118003_T02 (Zea mays), 3'ss of exon 2
gaagtacatttgattatatt--gtaaatgt-tcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
       | || | |||     | ||||    |  | ||   || ||   |   |    |  ||   || |  |   ||         | |||  |    ||||||||  | |||||||||   ||  |||| |||||||||||||||||||||||||| |||||||| || || ||  
-----gtacttaactatgcgaagcaaataaaccgatctgggctgagacacaagagagtttgatgcctttatcgttaactc-------ttttgttctgcttcagGAAGACGTCGATCTCATGAAAAGTTTGAACTTTGATGCCTACCGGTTCTCAATCTCATGGTCCAGGATCTTCCCGG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
----------------------------gaagtacatttgattatattgta-aatgttcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
                              ||| ||| |   ||  || ||   || | |  |  | |||   |  |       || ||    || | ||  |      |    |     ||||  ||||||||| | || ||||||   ||  |||||||||||||||||||||| |||||||| |||||||| || || ||| 
gtactgctccttattatatgacaatgctagagtccatctatctaggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacatttt-cagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g02680.t01 (Vitis vinifera), 3'ss of exon 2
-gaagtacatttgattatattgtaaatgttcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
     ||  | |  || |    || || |  | | ||| |  |  |||  ||||  |   | ||            || ||   |||   |   || ||||||||||||||| || |||   || || |||||||| || ||||| ||||||||||| |||||||| ||||| ||| 
gtttttaagtcttttttttaattatatatataatctgtttcatttttgccttgtttcaaatatttgaagaaataattgaaaactactg-atgtgttaacagGAAGATATAGACCTGATGAAGAGTCTTAATTTTGAAGCATACCGCTTCTCAATCTCATGGTCCAGGATTTTCCCAG

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|213604894|gb|DB960575.1|DB960575
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|209710515|gb|BW662051.1|BW662051
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|193650337|gb|FK598092.1|FK598092
EST:     CAAATAATGGCACGGGAGGAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTAACCGGTTACT
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTA-CCGGTT-CT
EST: gi|208079829|gb|GD874099.1|GD874099
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCAT
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCAT
EST: gi|213619687|gb|DB965633.1|DB965633
EST:     CAAATAATGGCACGGGAGAAGTTTCT-TTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|193500052|gb|FK463933.1|FK463933
EST:     GAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: GAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|208291083|gb|GE081551.1|GE081551
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|193383973|gb|FK351378.1|FK351378
EST:     TTCTGTTGATCAGTACCATCGCTAC-AA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: TTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|208211522|gb|GE014025.1|GE014025
EST:     AAATAATTGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: AAATAA-TGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|193363574|gb|FK331298.1|FK331298
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|193709892|gb|FK642142.1|FK642142
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|208110084|gb|GD907214.1|GD907214
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|193660704|gb|FK606428.1|FK606428
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|192332517|gb|FK025622.1|FK025622
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|298166439|gb|HO009878.1|HO009878
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|209702642|gb|BW652737.1|BW652737
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|207745315|gb|GD715417.1|GD715417
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|209718599|gb|BW674725.1|BW674725
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA
EST: gi|208092374|gb|GD885491.1|GD885491
EST:     CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA                         GAAGATATAGATCTCATGGCCAGCCCGAATTTTGATGCCTACCGGTTCTCA
genomic: CAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAAgtaagtgact ... aatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
                                 aataaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtacatttgattatattgtaaatgttcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA

- - - - - - - - - - - - - - - - - - - - gtgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaataaa