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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggccattctcttgtatttagttaatttattcttgcaattaacaacagtgctgacaagtagaataagagagtattttctcataattttctttggattggttaagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTCAATGTAAGGAAGAAGGCTGAAAACATTGTGTCGCTTTTGAATGATAAAG

Basic information

species Glycine max
transcript GLYMA17G35000.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G35000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g00640.t01 (Vitis vinifera), 3'ss of exon 7
gtaagggccattctcttgtatttagttaa-tttattcttgcaattaacaacagtgctgacaagtagaataagagagtattttctcataattttctttggattggtt---aagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTCAATGTAAGGAAGAAGGCTGAAAACATTGTGTCGCTTTTGAATGATAAAG
||| |     ||||||  ||||  || || |||   | | |||||   | || ||   | ||  ||  | | | | | ||| |      ||| || ||   |  ||   ||| |||||||  | ||||| ||||| ||||| | ||| |||||||| ||| ||||||| |||||||||||||||| ||||||| | ||||||||| | ||||
gtatgaattcttctctactattctgtgaactttgcccatacaattcttagcaatgactaaaataaggttgaaaaattgtttccaacatgtttcctctgttcttcttgtgaagTCACTTTCAGGATTTGAGTATGTTGAACCAAATGGGAAGGATGTTGGAATCAATGTGAGGAAGAAGGCTGAAACCATTGTGGCTCTTTTGAATAACAAAG
















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|254336972|gb|GR843151.1|GR843151
EST:     GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCT                         GCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
genomic: GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCTgtaagggcca ... attggttaagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
EST: gi|192323821|gb|FK015617.1|FK015617
EST:     GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCT                         GCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
genomic: GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCTgtaagggcca ... attggttaagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
EST: gi|192330169|gb|FK020514.1|FK020514
EST:     GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCT                         GCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
genomic: GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCTgtaagggcca ... attggttaagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
EST: gi|254331977|gb|GR843720.1|GR843720
EST:     GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCT                         GCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
genomic: GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCTgtaagggcca ... attggttaagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTC
EST: gi|193497575|gb|FK460807.1|FK460807
EST:     GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCT                         GCACTTTCTAGTTTTGAATATGTCGAA
genomic: GATCTGAACGTGCGGTTGATGACATTATAGAACATACTTTTCAGATATCTgtaagggcca ... attggttaagGCACTTTCTAGTTTTGAATATGTCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgacaagtagaataagagagtattttctcataattttctttggattggttaagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTCAATGTAAGGAAGAAGGCTGAAAACATTGTGTCGCTTTTGAATGATAAAG
 tgctgac  putative branch site (score: 2)
                      tattttctcataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggccattctcttgtatttagttaatttattcttgcaattaacaacagtgctgacaagtagaataagagagtattttctcataattttctttggattggttaagGCACTTTCTAGTTTTGAATATGTCGAACCTAGTGGTAAGGATGTGGGACTCAATGTAAGGAAGAAGGCTGAAAACATTGTGTCGCTTTTGAATGATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG