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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaacttttctattctgtttggaatttagctcatgtgttgttttataacattgtaacaatcgagtttggatatgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG

Basic information

species Glycine max
transcript GLYMA12G15470.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 4
gtatgaacttttctattctgtttggaatttagctcatgtgttgttttataacattg-taacaatcg-agtttggatatgatgttta----gATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG
||||| | |  | |  | | |   | |||| ||  || | |  |||| |   | |  | ||  |   |||  |   |  ||| |||    ||| ||||||||  | || ||||| ||||| |  |  || |||||||||||||||||||||||||||||| || ||
gtatgtaatgattttgtttctccaggattt-gcatatttttccttttttggtactcctgaccctgatagtaagtgaaaaatgcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG
















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|208291209|gb|GE092863.1|GE092863
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|10237492|gb|BE806380.1|BE806380
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|208175296|gb|GD975963.1|GD975963
EST:     CTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: CTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|37994214|gb|CF805960.1|CF805960
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|192301989|gb|FG995159.1|FG995159
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|193431643|gb|FK395149.1|FK395149
EST:     TGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: TGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|208102284|gb|GD897767.1|GD897767
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAAGGGGAATTAAGCATATAT
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTA-GGGGA-TTA-GCATATAT
EST: gi|207840066|gb|GD810595.1|GD810595
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATAT
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATAT
EST: gi|193514122|gb|FK466980.1|FK466980
EST:     GAACCAGAGAATGCCTCTCATCTACGTGAAACTGTATACATATCAA                         ATCTTCAGGGGATTAGCATATATCCATACCGCCCTGCGAGTTTGCCATAGG
genomic: GAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|193567659|gb|FK527356.1|FK527356
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGGAGTTTTGCCATA
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGG-AGTTT-GCCATA
EST: gi|254341725|gb|GR852862.1|GR852862
EST:     CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: CTATGAACCAGAGAATGCCTCTCATCTATGTGAAACTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
EST: gi|193588938|gb|FK540980.1|FK540980
EST:     CTGTATACATATCAA                         ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG
genomic: CTGTATACATATCAAgtatgaactt ... tgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcatgtgttgttttataacattgtaacaatcgagtttggatatgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG
                       ttgtaac  putative branch site (score: 2)
             ttttataacattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaacttttctattctgtttggaatttagctcatgtgttgttttataacattgtaacaatcgagtttggatatgatgtttagATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC