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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTAAAAATTGTCCGTGGTATTAAGAAGTATCGAGAAGCAGCCATGATAGAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaattttaacttaaatttgtcacgtatgcatactacaatgaaaatccttgattccattgcattggttaaatgggcttattccttgcag

Basic information

species Glycine max
transcript GLYMA17G13440.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 5'ss of exon 3
CCGTAAAAATTGTCCGTGGTATTAAGAAGTATCGAGAAGCAGCCATGATAGAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaattttaacttaaatttg--tcacgtatgcatactacaatgaaaa------------tccttgattccatt--gcattggttaaatgggcttattccttgcag
| |||||||||||||||||| | ||||| || || || || || ||||| ||||||||  || ||||||||||||||||||| || ||||| ||||||||||||||| | |    | |  |||   ||| | ||   || |   |||||              |||  |||||  ||  |||  ||||||||     ||||||||||||
CAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTATGATTGAAATTGAAATGCTGCAACAGCTTGGTAAACATGACAAAGGTGGCAATCGgtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcag

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 4
CCGTAAAAATTGTCCGTGGTATTAAGAAGTATCGAGAAGCAGCCATGATAGAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt----------ttaact--taaatttgtcacgtatgcatactacaatgaaaatccttgattccattg-cattggttaaatgggcttattccttgcag
|||| ||||||||||||||||||||||||||||| || || |||||||| |||||||| || || |||||||||| |||||| || || || |||||||||| |||  ||          ||||||  | ||  || ||| | |    |||   || |   |   | |     ||| || |||||||||| | |||||| ||||||
CCGTCAAAATTGTCCGTGGTATTAAGAAGTATCGTGAGGCTGCCATGATTGAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgtttactagtgttgttaactccttaacctgccac-tgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcag
















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|209715198|gb|BW668526.1|BW668526
EST:     GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCG                         TTGTGTGCAAAT
genomic: GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAAT
EST: gi|207776596|gb|GD747468.1|GD747468
EST:     AGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
genomic: AGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
EST: gi|192295348|gb|FG986002.1|FG986002
EST:     GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
genomic: GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
EST: gi|17518814|gb|BM187856.1|BM187856
EST:     GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
genomic: GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
EST: gi|9986568|gb|BE660676.1|BE660676
EST:     GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
genomic: GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
EST: gi|23064326|gb|BU579099.1|BU579099
EST:     GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTAT
genomic: GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTAT
EST: gi|9901661|gb|BE610629.1|BE610629
EST:     GAAATAGATGTGTTGCAACAGCTTGGTAAACACGATAAACGAGGCAATCG                         TTGTGTGCAAATACGGGACTCGTTTGACTATCGTCATCATATCTGTATT
genomic: GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
EST: gi|23064408|gb|BU579181.1|BU579181
EST:     GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATC
genomic: GAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaatt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTAAAAATTGTCCGTGGTATTAAGAAGTATCGAGAAGCAGCCATGATAGAAATTGAGGTGTTGCAACAGCTTGGTAAACACGATAAAGGAGGCAATCGgtaagtaattttaacttaaatttgtcacgtatgcatactacaatgaaaatccttgattccattgcattggttaaatgggcttattccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG