Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattcacttatccatcttttttcttttttttttttttctgttgtcaattatgtttcagttaaaactatttggaatttaactttttaatgtgtttagtctgttcaatttatcaattgtttgtttttggattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAAGACATGGAGGATTTTGGTGGTTTTGCAACTCTCAAGTCTCAGGGTGATT

Basic information

species Glycine max
transcript GLYMA06G43930.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0030g01480.t01 (Vitis vinifera), 3'ss of exon 16
gtatgtattcacttatccatcttttttcttttttttttttttctgttgtcaattatgtttcagttaaaactatttggaatttaactttttaatgtgtttagtctgttcaatttatcaattgtttgtttttggattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAAGACATGGAGGATTTTGGTGGTTTTGCAACTCTCAAGTCTCAGGGTGATT
                                               || || |  ||||  | | | |    |  | || || |     ||| | |||  | | ||| |  ||   |   | |  | ||| |   | ||||| || ||  | |||||||| ||||| ||||| ||||||||||| ||||| || || || |||||||||||  |||  | |    ||||||     ||| 
-----------------------------------------------gtaaagtg-gtttaggcttatatatatatgtatatagcaaaacaattttttttctttcttcta--tactgaagatctactattgaa---agcagGAGCCTGAAATTGAATATGTTGAAGGCTATGAAGAACTTGAAGAAGAAGATGATATTGAAGATTTTGGTGGCCTTGAGATTGATGAGTCTCTCAAGGATG

upper sequence: GLYMA06G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g09220.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtattcacttatccatcttttttcttttttttttttttctgttgtcaattatgtttcagttaaaactatttggaatttaactttttaatgtgtttagtctgttcaatttatcaattgtttgtttttggattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAAGACATGGAGGATTTTGGTGGTTTTGCAACTCTCAAGTCTCAGGGTGATT
                                               || || |   ||    ||| |  ||| |  |    |||  |||      |||  ||| |    | ||   |   | |  | ||| |   | ||||| || ||  | |||||||| ||||| ||||| ||||||||||| ||||| || || || |||||||||||  |||  | |    ||||||     ||| 
-----------------------------------------------gtaaagtggtttaggcttatatatatatatatcaaaacaattt------ttttttctttcttctatactgaagatctactattgaa---agcagGAGCCTGAAATTGAATATGTTGAAGGCTATGAAGAACTTGAAGAAGAAGATGATATTGAAGATTTTGGTGGCCTTGAGATTGATGAGTCTCTCAAGGATG
















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|193338548|gb|FK304735.1|FK304735
EST:     TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAG                         GAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
genomic: TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAGgtatgtattc ... gattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
EST: gi|193484164|gb|FK449820.1|FK449820
EST:     TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAA                         GAACCAGAAGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
genomic: TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAGgtatgtattc ... gattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
EST: gi|193718636|gb|FK652606.1|FK652606
EST:     TTCTTGATATGGAGAAACTTCAAGTTGCTGATGAAGAAGAGGATGAAGAG                         GAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
genomic: TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAGgtatgtattc ... gattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
EST: gi|208227168|gb|GE024185.1|GE024185
EST:     TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAG                         GAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
genomic: TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAGgtatgtattc ... gattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
EST: gi|208306599|gb|GE104468.1|GE104468
EST:     TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAA                         GAACCAGAAGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA
genomic: TTCTTGATATGGAGAAACTTCAAATTGCTGATGAAGAAGAGGATGAAGAGgtatgtattc ... gattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatgtgtttagtctgttcaatttatcaattgtttgtttttggattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAAGACATGGAGGATTTTGGTGGTTTTGCAACTCTCAAGTCTCAGGGTGATT
 ttttaat  putative branch site (score: 3)
                      aatttatcaattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattcacttatccatcttttttcttttttttttttttctgttgtcaattatgtttcagttaaaactatttggaatttaactttttaatgtgtttagtctgttcaatttatcaattgtttgtttttggattgaacagGAACCAGAGGTAGAATATGTAGAAGGTTATGATGAACTTGAAGAGGAAGAAGACATGGAGGATTTTGGTGGTTTTGCAACTCTCAAGTCTCAGGGTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG