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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaaagttcttctgtcatctctaaagcactatttatttaaaatcatcaatacataaggatcaaccatttcacacactattactagtcaattttg...

Basic information

species Glycine max
transcript GLYMA06G41600.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os04g53760.2 (Oryza sativa), 5'ss of exon 11
TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaaagttcttctgtcatctctaaagcactatttatttaaaatcatcaatacataaggatcaaccatttcacacactattactagtc-aattttg-----------
| | ||  ||| ||| ||||||||    |  |  || ||||||||||| || ||||||||||| ||||| || || |||||||| |||||||| |||||||||   | ||  ||   ||  || |  | ||| | |  |       ||| |||  | ||| ||| ||  |  | ||  | |     | ||  | || |||            
TTCCTTCTCATATGACAAAGTTTTCGATCACGGTGCTTCACAAGAAGATGTGTTTGTGGAAATGTCACAACTAGTTCAAAGTGCACTTGATGGGTACAAGgta---tgaatatttcacta-caacaatgaagtattggt------gaataatctgttcatgaggttc--ctgtctctaataactcaaatatcctaactttattttttttatt

upper sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 10
TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaaagttcttctgtcatct-ctaaagcactatttatttaaaatca-tcaatacataaggatcaaccatttcacacactattactagtcaattttg
  | ||  ||| ||| || ||||||   |  |  || ||||| ||||| || ||||||||||| || || || || |||||||| |||||||| ||||||||| |     |    |    | || | |||| | |   | |||| |  || | |    |  | |      |  || |    |  |||| | |    ||  ||
CTCCTTCTCATATGACAAGGTTTTTGACCATGGTGCGTCACAGGAAGATGTGTTTGTGGAAATATCGCAACTAGTCCAAAGTGCCCTTGATGGGTACAAGgtactaacttatgcatgacattatatgctaatgtatagtatattaagtatgaattgtcatcttacctgttaaaatattgtcctttattcccaac--atgatg

upper sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 10
lower sequence: AT4G27180.1 (Arabidopsis thaliana), 5'ss of exon 11
TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaaagttcttctgtcatctctaaagcactatttatttaaaatcatcaatacataaggatcaaccatttcacacactattactagtcaattttg------------------------------------------------------------------------------------------
|  ||| ||||||||||| ||||||   |||   |||||||||||||| |||||||| || ||||| || ||||| || || ||||||||||||||||||||| | |     | |||  |     | |||  | || |||| |||   || ||| ||    |      |   ||||| |   ||||  | || ||  |                                                                                            
TTGTTTCACATTTGATAAGGTTTTTGTGCCAAGTGCATCACAAGAAGATGTTTTTGTAGAGATTTCTCAACTTGTCCAGAGCGCTCTTGATGGTTACAAGgtactatc----tgctttagcttagtttaactccctgtttacttatg-tcttcattattcgattcctcaaattttcagagtgtatt-ttggtaaaactgtctaactggtcaataaaagcacatgaatgatgaataatgttatgtttcactgtaccttcttggactaaaggttctattacacaattttcag

upper sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 11
TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaaagttcttctgtcatctctaaagcactatttatttaaaatcatcaatacataaggatcaaccatttcacacactattactagtcaattttg
|||||| ||||||||||| |||||| | ||    |||||||||||||| || ||    || ||||| || ||||| ||||||||||| |||||||||||||||| | |||  | |   || ||     |||| ||||| |   |   |   |   |    ||  |  || |   |   |  |  ||  |||         
TGCTTTCACATTTGATAAGGTTTTTGCGCCGACTGCATCACAAGAAGATGTCTTCACTGAGATTTCTCAACTTGTTCAAAGTGCTCTCGATGGTTACAAGgtaact-aaatctgcaaatggcaa----aaagtactatgtgcgtttcactgtttgt-tggaataactaagctgatagaatccattttatag---------

upper sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 5'ss of exon 10
TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaa--agttcttctgtcatctctaaagcactatttatttaaa---atcatcaatacataaggatcaaccatttcacacactattactagtcaattttg
| | || || || || ||||| ||||  || || ||| | ||| | ||||| ||||| ||||| ||||||||||| || |||||||| |||||||| |||||||| || |   | ||   | |||   ||   |  | |||||  || |    |  |   |  ||| | |    ||    ||||  || |  ||  | ||||   
TTCGTTCACCTTCGACAAAGTGTTTATGCCTGATGCACCGCAACAGGAAGTCTTTGTAGAAATCTCACAGCTTGTACAGAGTGCTCTGGATGGTTATAAGgtaatctacattggctccgatttcagtcct---gtcccatttacatagatgtgttctgtgtggatatgcaatttcctgaacacattctgtatctgcttaattg--

upper sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ35821 (Selaginella moellendorffii), 5'ss of exon 10
TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaaagttcttctgtcatctctaaagcactatttatttaaaatcatcaatacataaggatcaaccatttcacacactattactagtcaattttg
    ||| | || || ||||| |||   || ||  |    |||||    || |||   ||||| || || ||||||||||||||||| ||||| |||||||||||| | ||   | | | |  |||    |   | | | || | |   |      |||    |  ||                                
CTTCTTTTCTTTCGACAAAGTGTTTGGTCCTGAAACTGGCCAAGAGAGCGTGTTTACAGAAATATCTCAACTTGTGCAAAGTGCTCTGGATGGATACAAGgtaattaagaaaagcgtatcttttct----actgccactcatatgatgacgctgtaacacttcg--cag-------------------------------

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|26057105|gb|CA800019.1|CA800019
EST:     TTTTTGTGGAAATTTCACAGCTTGTACAAAGTGCTCTTGATGGTTACAAG                         GTTTGCATCTTTGCCTATGGTCAGACAGGGTCAGGGAAAACCTATACAATG
genomic: TTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaa ... tcttcttcagGTTTGCATCTTTGCCTATGGTCAGACAGGGTCAGGGAAGACCTATACAATG
EST: gi|207783369|gb|GD755901.1|GD755901
EST:     ATGGTTACAAG                         GTTTGCATCTTTGCCTATGGTCAGACAGGGTCAGGGAAGACCTATACAATG
genomic: ATGGTTACAAGgtaatttaaa ... tcttcttcagGTTTGCATCTTTGCCTATGGTCAGACAGGGTCAGGGAAGACCTATACAATG
EST: gi|7591541|gb|AW707272.1|AW707272
EST:     TTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAG                         GTTTGCATCTTTGCCTATGGTCAGACAGGGTCAGGGAAGACCTATACAATG
genomic: TTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaa ... tcttcttcagGTTTGCATCTTTGCCTATGGTCAGACAGGGTCAGGGAAGACCTATACAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTTTACATTTGATAAAGTTTTTACACCAGAGGCATCACAAGAAGAAGTTTTTGTGGAAATTTCACAGCTTGTGCAAAGTGCTCTTGATGGTTACAAGgtaatttaaaagttcttctgtcatctctaaagcactatttatttaaaatcatcaatacataaggatcaaccatttcacacactattactagtcaattttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG