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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGTTGGTGGTGGAGATGGCGGTGTACTAAGGGAAGTAGCCCGCCATAGCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGATgtaagtaaggccatatttcaatcattaatatagctatttcattattcagaaaaaaatactgttatggttatttgtag

Basic information

species Glycine max
transcript GLYMA06G13210.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13210.3 (Glycine max), 5'ss of exon 6
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 5'ss of exon 7
AGTTGTTGGTGGTGGAGATGGCGGTGTACTAAGGGAAGTAGCCCGCCATAGCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGATgtaagtaa--ggccatatttcaatcattaatat-----------agctatttcattattcagaaaaaaatactgttatggttatttgtag
 ||||||||||| || ||||| ||||| ||  | ||  |  | |||||||| ||||| ||   ||||||||| ||||||||||| ||||||||||| |||||||||    ||   | |      |||   |||           || ||| |  |   |||||||     | |  | ||||   ||||||
TGTTGTTGGTGGAGGTGATGGTGGTGTTCTTCGAGAGATTTCTCGCCATAGTTCTGTTGAGGTTATTGATATCTGTGAGATAGACAAGATGGTTATAGATgtaagtttttggttttgtgcttgccatatgtatgaacaatttttagttatgttctatctcagaaagtgggatttctgtggtc--ttgtag

upper sequence: GLYMA06G13210.3 (Glycine max), 5'ss of exon 6
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 6
AGTTGTTGGTGGTGGAGATGGCGGTGTACTAAGGGAAGTAGCCCGCCATAGCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGATgtaagtaaggccat--------atttca-atcattaa--tatagctatttcattat--tcagaaaaaaatactgtta--tggttatttgtag
 |||||||||||||| ||||| || || || |||||| |  | || ||||||||||| || | ||||||||||||||||||||||||||||||||| |||||||||   |   |        ||||||  | ||||     |||||  |||||| |  |  |||  || | || |    || ||||||||||
GGTTGTTGGTGGTGGTGATGGTGGGGTTCTTAGGGAAATTTCTCGTCATAGCTCTGTTGAGCTTATTGATATTTGTGAGATAGATAAGATGGTTATAGATgtaagtggtggtgtgatgtaccatttcatgttattaggtcttagcttgttcattgtgatttgaaccaactcctttctgttgtttatttgtag
















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|151394500|gb|EV264371.1|EV264371
EST:     GCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGAT                         GTTTCTAGGAAGTTTTTTCCACAGTTGGCTGTTGGGTTTGAAGATTCTCGA
genomic: GCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGATgtaagtaagg ... ttatttgtagGTTTCTAGGAAGTTTTTTCCACAGTTAGCTGTTGGGTTTGAAGATTCTCGA
EST: gi|17963401|gb|BM270150.1|BM270150
EST:     GCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGAT                         GTTTCTAGGAAGTTTTTTCCACAGTTAGCTGTTGGGTTTGAAGATTCTCGA
genomic: GCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGATgtaagtaagg ... ttatttgtagGTTTCTAGGAAGTTTTTTCCACAGTTAGCTGTTGGGTTTGAAGATTCTCGA
EST: gi|208218386|gb|GE020436.1|GE020436
EST:     GCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGAT                         GTTTCTAGGAAGTTTTTTCCACAGTTAGCTGTTGGGTTTGAAGATTCTCGA
genomic: GCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGATgtaagtaagg ... ttatttgtagGTTTCTAGGAAGTTTTTTCCACAGTTAGCTGTTGGGTTTGAAGATTCTCGA
EST: gi|208104637|gb|GD905020.1|GD905020
EST:     AAGATGGTTATTGAT                         GTTTCTAGGAAGTTTTTTCCACAGTTAGCTGTTGGGTTTGAAGATTCTCGA
genomic: AAGATGGTTATTGATgtaagtaagg ... ttatttgtagGTTTCTAGGAAGTTTTTTCCACAGTTAGCTGTTGGGTTTGAAGATTCTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGTTGGTGGTGGAGATGGCGGTGTACTAAGGGAAGTAGCCCGCCATAGCTCTGTGGAACATATTGATATTTGTGAGATAGATAAGATGGTTATTGATgtaagtaaggccatatttcaatcattaatatagctatttcattattcagaaaaaaatactgttatggttatttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG