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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctattactgaataaaaatatcaaaagtattttagtgtgtgatggatttttgaagtttccttggtagtgtctcacaattttttggctttttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT

Basic information

species Glycine max
transcript GLYMA13G38690.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 3
ctctattactgaataaaaatatcaaaagtattttagtgtgtgatggatttttgaagttt-----ccttggtagtgtctcacaattttttggctttttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
   |  |      |     ||    |  |||     |   | |  | || |   || ||       | |||| |  || |    || || |     |  ||| |||||||| |||||||||| |||||||||||| | ||||||||||
--ttcctttcatgtgggtttactggat-tatggagctaactaacagtttctctgagcttatgcttatgggtaatagctaaatgcttctttgacacct--atgcagTTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT

upper sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 3
ctctattactgaataaaaatatcaaaagtattttagtgtgtgatggatttttgaagt-ttccttggtagtgtctcacaa-ttttttggctttttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
 |    |  |   |   | | || ||   | || |   ||  |||  | |   |||  || ||      || || |  | |||| |     || || || || | ||||||||||||||||||||||||||||||||||||||||
ttgctcttttatgtttcattttccaag--aattaaccttgcaatgactatcctaagcatttctcaacgatgactaatgagttttctctgacttcttctgcagCTTGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
















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|58023225|gb|CX709966.1|CX709966
EST:     TCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: TCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
EST: gi|22524282|gb|BU083093.1|BU083093
EST:     ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
EST: gi|58020255|gb|CX706997.1|CX706997
EST:     GGACACCAACTTCATCAATTTCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: GGACACCAACTTCATCAATTTCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
EST: gi|14125427|gb|BG789865.1|BG789865
EST:     ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
EST: gi|58020043|gb|CX706785.1|CX706785
EST:     TGTTTTGGTGGACACCAACTTCATCATTTTCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: TGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
EST: gi|13788867|gb|BG651458.1|BG651458
EST:     ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
EST: gi|21602514|gb|BQ612845.1|BQ612845
EST:     ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
EST: gi|13788871|gb|BG651462.1|BG651462
EST:     ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAA                         TTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
genomic: ATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAAAATAAAgtgagttgct ... ttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttttgaagtttccttggtagtgtctcacaattttttggctttttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT
                        gtctcac  putative branch site (score: 3)
                                 ttttttggcttttttt  putative PPT
                                          tttttttatgta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctattactgaataaaaatatcaaaagtattttagtgtgtgatggatttttgaagtttccttggtagtgtctcacaattttttggctttttttatgtagTTGGATCTGGAGAAAGGGATGATGGACTGCTTATATGCAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA