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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagattttggtgtggtatttatgatgtacaaacccttctttgccaattgtaaaattgctatttgatgtctattgattacag

Basic information

species Glycine max
transcript GLYMA09G39150.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39150.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 5'ss of exon 3
CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagattttggtgtggtatttatgatgtacaaacccttctttgccaattgtaaaattgctatttgatgtctattgattacag-----
| | || || |||||||| |||||||| || ||| | |  |||||| ||||||||| ||||||| | ||||| ||||||||||||||     | |||| | |  | ||   | | |  |   |   |    | |||| | ||| | |||  |    | |   ||  |      
CTATTTTCACTTTGTTCATGAGTTTGTAACTATACTTATGGACTCTGCAATTTTGTTCTTTGGGATCTTGCCTTGGTTTTGGAAGgtacatatctggtttcg-gtatacagtat-ctcattttgaatatagagttgttacattacaattgtaaagttttcatttttaccttag

upper sequence: GLYMA09G39150.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 3
CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagattttg-gtgtggtatttatgatgtacaaacccttctt-------tgccaat---tgtaaaattgctatttga---tgtctattgattacag
|||||||||||||||||| ||||  || || ||| | |  |||||| ||||||||| |||||| |||||||| |||||||||||||| ||    ||  | ||    |||||||   ||  |||| |         | |  ||   |  |||||   | |       ||  |  ||| | |||
CCACTTCCATTTTGTTCATGAGTGCGTTACTATATTAATGGACTCTGCAATTTTGTTCTTTGGAGTATTGCCTTGGTTTTGGAAGgtaagtgaatgcatttgtggattatgataggcaccccctaccccccaacatacagatgcatacaaaataattgtgcccatttgctttgtgactgcag
















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|15202361|gb|BI425361.1|BI425361
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
EST: gi|192302658|gb|FG994896.1|FG994896
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
EST: gi|193425164|gb|FK389893.1|FK389893
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
EST: gi|4396612|gb|AI495609.1|AI495609
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
EST: gi|209708354|gb|BW683944.1|BW683944
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
EST: gi|209723765|gb|BW657734.1|BW657734
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
EST: gi|213594940|gb|DB971799.1|DB971799
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
EST: gi|193346112|gb|FK310528.1|FK310528
EST:     TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAG                         AAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA
genomic: TGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagatttt ... ttgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACTTCCATTTTGTTCACGAGTTTGTGACAATAGTGACAGACTCTACAATTTTGTACTTTGGGGTATTGCCCTGGTTTTGGAAGgtgagattttggtgtggtatttatgatgtacaaacccttctttgccaattgtaaaattgctatttgatgtctattgattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG