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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGCGTATATACGAAGAGTATTTGGCAGTTCCTGTCATAAAGGGTAAGAAAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtctgattcttgcataaacagttgtgttattttaatggtgtaagctgcttataaaattttgatgttcaattttgctag

Basic information

species Glycine max
transcript GLYMA19G40930.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G40930.4 (Glycine max), 5'ss of exon 8
lower sequence: AT3G62120.1 (Arabidopsis thaliana), 5'ss of exon 7
TAGGCGTATATACGAAGAGTATTTGGCAGTTCCTGTCATAAAGGGTAAGAAAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtctgattcttgcataaacagttgtgttattttaatg-gtgtaagctgcttataaaattttgatgttcaattttgctag
  | || ||||| ||||| ||| | |||||||| ||  | || |||| ||| |||||   ||||||||||||||||||||| |||||||| ||||| ||||||| |      || |||     | | ||    | ||||  || | ||   ||   | | || ||  ||  ||  |||||  |||
CCGTCGCATATATGAAGAATATCTTGCAGTTCCAGTTGTGAAAGGTATGAAGAGTGAAAATGAGAAGTTTGCTGGTGGACTTTACACTACAAGTGTAGAGgtatgtaatc--tttttgttctgagacttaaccttttttcttgtgggtttactctctgtgaagtt--gaactttgatttta-tag

upper sequence: GLYMA19G40930.4 (Glycine max), 5'ss of exon 8
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 5'ss of exon 8
TAGGCGTATATACGAAGAGTATTTGGCAGTTCCTGTCATAAAGGGTAAGAAAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatg--tctgatt------cttgcata--aacagttgtgt-tattttaatgg--tgtaagctgctta---taaaattttgatgttcaattttgctag--------------------------------------
||| |||||||| |||||||| |||||  ||||||| |||||||||||||| |||||| | |||||||||||||||||| | ||||| || ||||||||||||  ||  | | |||      ||||||    | |  ||||   |  |  ||||   || || | | ||    |||   ||   ||||| ||  |   ||                                      
TAGACGTATATATGAAGAGTACTTGGCGATTCCTGTTATAAAGGGTAAGAAGAGTGAGATGGAGAAGTTTGCTGGTGGATTTTACACAACAAGTGTTGAGgtacttgatttttatttatctgcttgcactccatcctttgtccatcatccaatgaattgcaaaccgtttgcattaactattctgtgttctatgatagaagtaaactgtgtaattatgtctgtgtttaccttttttcag

upper sequence: GLYMA19G40930.4 (Glycine max), 5'ss of exon 8
lower sequence: PP1S7_175V6.1 (Physcomitrella patens), 5'ss of exon 6
TAGGCGTATATACGAAGAGTATTTGGCAGTTCCTGTCATAAAGGGTAAGAAAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtctgattcttgc-ataaacagttgtgttattttaatggtgta--agctgcttataaaattttgatgttcaattttgctag--------------
  |  |  |||| || |||    | || ||||||||||| ||||||   ||||||||| | ||||||||||||||||| || || ||||| | ||| ||||||    |   ||  ||   ||  | |||  |   ||||   |  |  |  |||  ||| ||     ||  ||  ||   |    |               
CCGCAGGGTATATGAGGAGCTCCTAGCCGTTCCTGTCATCAAGGGTGTTAAAAGTGAGGTCGAGAAGTTTGCTGGTGGTCTGTATACTACTACTGTAGAGgtactccttccatctttatgatgtatagtgattcgatttggttcatccactagcatctt-tattgcattactgaccacgctcctcaagcttctggtttgca

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|193568519|gb|FK525192.1|FK525192
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACTAGTGTTGGG                         GCATTTATTCCAAACACTGGCCGTGGTATACAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|208144861|gb|GD943452.1|GD943452
EST:     ACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: ACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|207831009|gb|GD805067.1|GD805067
EST:     GTGAGTCTTTGAGAAGTTTGTCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: GTGAG-C-TTGAGAAGTTTG-CTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|193659280|gb|FK605947.1|FK605947
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGG
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGG
EST: gi|193330683|gb|FK296175.1|FK296175
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|193377536|gb|FK341060.1|FK341060
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACTAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATACAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|208199816|gb|GD998559.1|GD998559
EST:     TACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: TACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|208174450|gb|GD968159.1|GD968159
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|207844905|gb|GD817456.1|GD817456
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|9899427|gb|BE608395.1|BE608395
EST:     CAAGTGAGCTGGAGAAGTTTGCTGGTGGACTCTACACTACCTGTGCTGAG                         GCATTTATTCCAAACACTGGATCG-GGTAT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGG-TCGTGGTAT
EST: gi|207734424|gb|GD713312.1|GD713312
EST:     AAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: AAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|193533168|gb|FK493688.1|FK493688
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACTAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATACAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|207758541|gb|GD726795.1|GD726795
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACTAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATACAAGGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGT
EST: gi|193382732|gb|FK347217.1|FK347217
EST:     AGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: AGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|208320376|gb|GE122097.1|GE122097
EST:     CTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: CTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|207783076|gb|GD751077.1|GD751077
EST:     GTGAGCTTGAGTAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: GTGAGCTTGAG-AAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|208315695|gb|GE110565.1|GE110565
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
EST: gi|208093213|gb|GD896396.1|GD896396
EST:     AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAG                         GCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT
genomic: AAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtct ... attttgctagGCATTTATTCCAAACACTGGTCGTGGTATCCAAGGTGCAACTTCTCATTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGCGTATATACGAAGAGTATTTGGCAGTTCCTGTCATAAAGGGTAAGAAAAGTGAGCTTGAGAAGTTTGCTGGTGGACTCTACACTACCAGTGTTGAGgtatatgtctgattcttgcataaacagttgtgttattttaatggtgtaagctgcttataaaattttgatgttcaattttgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA