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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCCCAACATGCTGCGAGACGTGCTGCTAGTTTTGTGCGAGGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaataaacctgatataatttcagttgtcagtttatggtagttagctgtaacactgaccagagattatgttatgcag

Basic information

species Glycine max
transcript GLYMA04G39250.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39250.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATCCCAACATGCTGCGAGACGTGCTGCTAGTTTTGTGCGAGGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaataaacctgatataatttcagtt-gtcagtttatggt---agttagctgtaaca-ctgaccagagattatgttatgcag
|| || |    |||||| || || || ||| |||||||| ||||||||||||||||||||||| | || |||||||||||  || | ||||||| |||  | ||  |  | |    ||| ||   ||||  || |    ||     || |  | |||   | | ||||| |  | |||
GGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAAgtgagtcttcaaattcttttggcatcattttaacagtccattgcctaagcgctttgcattatctggatatatattatttgttacag

upper sequence: GLYMA04G39250.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G64650.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATCCCAACATGCTGCGAGACGTGCTGCTAGTTTTGTGCGAGGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaa------gtaataaacctgatataatttcagttgtcagtttatggtagttag-ctgtaacactgaccagagattatgt-tatgcag----
|| || | |  ||| || ||| | |||||| | |||||  ||||||||||||| ||||||||| | ||||||||| ||||| |||| ||||||| |      |||       |  |    |||   |||  |  || |  ||   |  ||||   ||   |  ||  ||| || | ||       
GGTTCACTAGCTGCAGCAAGAAGAGCTGCTGGGTTTGTTAGAGGAGATGATGTACTTCACAAGATTTTTACAGAATTGGCTCATCGATACAAgtgaattctcgtatctcgttttttccttttttttttgggatcttttcctatgcactctgttttaccagctggatgttacgtatgtgttaacag

upper sequence: GLYMA04G39250.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 5'ss of exon 4
GGATCCCAACATGCTGCGAGACGTGCTGCTAGTTTTGTGCGAGGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaataaacctgatataatttcagttgtcagtttatggtagttagctgtaacactgaccagagattatgttatgcag
|| || |    |||||| || ||||| ||    ||||||||||| ||||||||  |||||||||| || || |||||||||||| | ||||||| | |  |||||||| |  | |||||||| ||  ||    |||  | | ||||| | ||    |  ||| | |  | |||
GGTTCTCTTTGTGCTGCAAGGCGTGCAGCAGCCTTTGTGCGAGGGGATGATGTGATTCACAAGCTATTCACTGAACTGGCTTATAGATACAAgtgaatcttaaacctgttgcattttcagttttctttt----gta--tggttgtaatattggatgggcattctctgtttcag

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|26268298|gb|CA819361.1|CA819361
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|298187006|gb|HO034155.1|HO034155
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCATATCGGTACAA                         GGGTAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192311623|gb|FK003106.1|FK003106
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192310244|gb|FK002600.1|FK002600
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGACTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192310245|gb|FK002601.1|FK002601
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGACTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192311622|gb|FK003105.1|FK003105
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|31470250|gb|CD412218.1|CD412218
EST:     GCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|20814760|gb|BQ299238.1|BQ299238
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCATATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|7587908|gb|AW703714.1|AW703714
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|298174461|gb|HO014606.1|HO014606
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCATATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTAGGATCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|23064422|gb|BU579195.1|BU579195
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|298189819|gb|HO038222.1|HO038222
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCATATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|14009072|gb|BG725667.1|BG725667
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|16343728|gb|BI969323.1|BI969323
EST:     GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA                         GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCCCAACATGCTGCGAGACGTGCTGCTAGTTTTGTGCGAGGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAAgtaagtaataaacctgatataatttcagttgtcagtttatggtagttagctgtaacactgaccagagattatgttatgcag

- - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT