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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttggcattattacattacaggcattatgcttttttggattgaagtcagattatatacttaatcggttagctgactcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA

Basic information

species Glycine max
transcript GLYMA19G35370.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G353548_T05 (Zea mays), 3'ss of exon 9
-catttg-gcattattacattacaggcattatgcttttttggat-tgaagtcagattatatacttaatcggttagctgactcaatg-gaatttgcc--ctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA-
 ||| || | ||| |  |  |||  | | |    ||| ||| || | | |   ||  |   | ||    | ||   | ||| | |  ||| || ||   ||||||||||||||||||| |||||||| ||||| ||  ||||| | |  ||||| ||||||||| || | || || | |||||  |  ||  | |  | || | |  
tcatatgtgaattgtacctgtacttgtact----tttgttgcatcttatgcttgagcagggaattg--tgatttcattacttactatgaacttaccaattttgcagTGAAATGGGTGCCCATTTTTCCCCATGTGGACGATTTCTTGTAGCCTGCGTTGCATGTTTGTTGCCTCAAACAGAAGGTGG-CCGTGGTAGCCAATTGCCT

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
lower sequence: AT1G04140.2 (Arabidopsis thaliana), 3'ss of exon 8
catttggcattattacattacaggcattatgcttttttggattgaagtcagattatata---cttaatcggttagctgactca-atggaatttgccctt-----tgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
    |   ||| |  | ||| |  | || | |  | || |||    || |   ||||||    ||   |  ||    ||   | |||   | ||   ||     |||||||| ||||| || |||||||| ||||| || |||| |||||| ||||||||||||||  |  |||| |||   ||  |||||||| | || || || |  
---gtaaaatt-tctccttatat-cgttgtacgatcttagatgatcgtgatgctatataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
lower sequence: AT5G43930.3 (Arabidopsis thaliana), 3'ss of exon 8
-----------catttggcattattacattacaggcattatgcttttttggat-tgaagtcagattatatacttaatcggttagctgactcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
             | |||     | | || |      |||  |||   ||  | ||| |  |  || ||   ||    |  ||      ||  ||    ||    | | |||||||||||| ||||||| ||| ||||| || |||| |||||| ||||||||||| ||| |  |||| |||   ||   |||||| ||| | || || | |
gcaaagctccttctctgggtccttgatatcattc-tgttacacttgaatgcctatgatgctaagttttactattggatgtatattgatatctctgcttctttttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 8
-catttggcattattacattacaggcattatgcttttttggattgaagtcagattatatacttaatcggttagctgactcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
  ||   | |||   |  | | |    || ||| |     | |     |       | |   | || | |||||  | | |    |         || ||||||||||||||| ||||| ||||| || || ||||||||||||||||||||||||||| ||||||| ||| | ||||| ||||| ||||| ||||| |  
atatcaagtatttgcatttcataaaatttctgcctagcctg-tcatccttgatccttgttacttatggtttagcatatttatgacacaactgtgattccagTGAAATGGGTGCACATTTATCACCTTGTGGGAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATTTGGAAGCTGATCCTGGATTGCAAACACAG

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 9
catttggcattattacattacaggcattatgcttttttggattgaagtcagattatatacttaatcggttagctgactcaatggaatttgccctttg--cagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
|| ||  ||   | | ||| |        ||   ||||| | |    |  | |||| |   |||    || ||    | |||    | ||     ||  ||||||||||||||| || |||||||| || ||| ||||| ||||||| |||||||| ||| || | |||      ||  | ||| || |       | | | 
caatttacaccctgaaattcctcttgacttgagattttgcaatcttttgtgtttatctg--taacatcttcgcgtgttgaatattgtgtggttcgtgagcagTGAAATGGGTGCGCACTTTTCACCTTGTGGTCGATTTCTAGCTGCGTGTGTTGCCTGTGTGTTGCCCATGGCGGATTCTGATTCACGGCGTGGGAATACG

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 8
catttggcattattacattacaggcattatgcttttttgga---ttgaagtcagattatatacttaatcggttagctgactcaatggaatttgccctttg--cagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
    |  |||  | |     || || |  |  ||||  | |   |||   | |    || || || ||   || | ||  | |||    | ||   |  |  ||||||||||||||| || |||||||| || ||| | ||| ||||||| |||||||| ||  || | ||     | ||  | ||  || |      || | | 
----tatcatggtaatcagtcaagcgt-gtatttttgagaaaatttgtgataattcaatctatttgatacctttggtggtttaatattgtgtggtgtgggagcagTGAAATGGGTGCGCACTTTTCACCGTGTGGTCGGTTTCTAGCTGCGTGTGTTGCTTGCGTGTTGCCTATGGTTGATTCTGAGTCACGTCGTGGAAATACG

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|208107336|gb|GD907923.1|GD907923
EST:     CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGTCTGCCTGTG
genomic: CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAG-CTGCCTGTG
EST: gi|207780572|gb|GD750855.1|GD750855
EST:     CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
EST: gi|193667497|gb|FK611009.1|FK611009
EST:     CATGCTGTTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
genomic: CATGCTG-TCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
EST: gi|26058982|gb|CA801896.1|CA801896
EST:     CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
EST: gi|21889859|gb|BQ743072.1|BQ743072
EST:     CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
EST: gi|207846186|gb|GD818569.1|GD818569
EST:     CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
EST: gi|26047106|gb|CA783997.1|CA783997
EST:     CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
EST: gi|12690329|gb|BG156665.1|BG156665
EST:     CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAG                         TGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT
genomic: CTTAATGCTGATAGATGTCGTCTAACCGTACCGCATGCTGTCCTCTGCAGgtaccttctg ... ccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcagattatatacttaatcggttagctgactcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
                         agctgac  putative branch site (score: 3)
                                         tttgcccttt  putative PPT
      attatatacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttggcattattacattacaggcattatgcttttttggattgaagtcagattatatacttaatcggttagctgactcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - -ggcatta
- - - - - - - - - -acaggca
- - - - - - - - - - - - - -tatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgactc