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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGTTTGCTTGGTAGATGACATGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaattcatatacaccctttcttcattttttgaggctaggttaggaattacgatgtctgaattgaagtcatgtttgtgcctgatattatgtattctctctctttttttcttttttggcag

Basic information

species Glycine max
transcript GLYMA04G03290.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03290.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 3
TGTGTTTGCTTGGTAGATGACATGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtac---ttctaattcatatacaccctttcttcattttttgaggctaggttaggaattacgatgtctgaattgaagtcatgtttgtgcctgatattatgtattctctctctttttttcttttttggcag
||||||||| |||| ||||   |||| || ||||||||||||||||||||||||| |||||| ||  ||||||| |    |    |||   |   |  | |  ||| ||    ||  |||| |   | |     | |    |  |   || | ||       |     ||| | |||   | || |||| |   ||| |||
TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgcttcttttctggttttctttcttgtcacttaaatagtttaggctccaagtctttcttttcatacagttttcttattaagatgagcatacatggagtcttattattgttttgtcccttg-cag
















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|298196538|gb|HO041281.1|HO041281
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
EST: gi|15814578|gb|BI786853.1|BI786853
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGTG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGTG
EST: gi|7795143|gb|AW780540.1|AW780540
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
EST: gi|58016809|gb|CX703551.1|CX703551
EST:     TCAAATGCTGTCAAAGTTCAG                         GCACAAGAA-TGGTNGAAAGAGGATTTCAAGGGCTCCAAG
genomic: TCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGT-GAAAGAGGATTTCAAGGGCTCCAAG
EST: gi|192334033|gb|FK026190.1|FK026190
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
EST: gi|298173637|gb|HO016973.1|HO016973
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGTGGTTGG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGTGGTTGG
EST: gi|193466704|gb|FK432111.1|FK432111
EST:     TGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATT
genomic: TGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATT
EST: gi|298179451|gb|HO027922.1|HO027922
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGTGGTTGGT
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGTGGTTGGT
EST: gi|298186858|gb|HO033957.1|HO033957
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAG
EST: gi|192323065|gb|FK016316.1|FK016316
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
EST: gi|192326921|gb|FK015148.1|FK015148
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
EST: gi|16996508|gb|BM085880.1|BM085880
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGT
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAGT
EST: gi|298173676|gb|HO017012.1|HO017012
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAG
EST: gi|41145774|gb|CK605985.1|CK605985
EST:     TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG                         GCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG
genomic: TGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaa ... tttttggcagGCACAAGAATTGGTGAAAGAGGATTTCAAGGGCTCCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGTTTGCTTGGTAGATGACATGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtacttctaattcatatacaccctttcttcattttttgaggctaggttaggaattacgatgtctgaattgaagtcatgtttgtgcctgatattatgtattctctctctttttttcttttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG