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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtgttttcctaatggtttcatgttttcttttcactttgtgtgtcttaactcaaatggttggttgatctttgactgaatgcaacctgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAAGAGACAGAAGAAGAGAAGAAGGCAGCAGAGGAACGGGCAGCTGCAGTGA

Basic information

species Glycine max
transcript GLYMA06G17930.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------gca-agtgttttcc-taatggtttcatgttttcttttcactttgtgtgtcttaactcaaatggt--tggttg--atctttgactgaatgcaacctgttc----ttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAAGAGACAGAAGAAGAGAAGAAGGCAGCAGAGGAACGGGCAGCTGCAGTGA
                                                    ||| |||  | |   |  || ||| ||| | |  || ||  ||  || | |    |  ||||||  |||||   |||| | |   |     |  | |||    |||||||| |||  ||||| |||||||||||||| ||||| ||  | || ||||| ||||| ||||| |||||||||||||| ||||| || || ||||| || |
gtcatacaaccctagccttgtcttgtttgcctgaaatctgtgaagtgttctagcatagtactgtgaattgtgatttgatgctgt--ttgcaaattacgtttttgtggttcaatggtgctggttaccatctctaatatatcatcatatcttctaatttcagGCTCCTGCAGCTGATGATGACGATGATGACGATGTTGACCTTTTTGGTGAGGAGACTGAAGAGGAGAAGAAGGCAGCTGAGGAGCGTGCTGCTGCTGTCA
















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|298175581|gb|HO018292.1|HO018292
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|7588414|gb|AW704210.1|AW704210
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|16106028|gb|BI893768.1|BI893768
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTCGTTCGGGGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|213617811|gb|DB959395.1|DB959395
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|208187245|gb|GD982167.1|GD982167
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|192328314|gb|FK020025.1|FK020025
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGTTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|9259946|gb|BE348093.1|BE348093
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|298194444|gb|HO041092.1|HO041092
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|208274596|gb|GE070230.1|GE070230
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|207732416|gb|GD708575.1|GD708575
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGA
EST: gi|18040877|gb|BM309171.1|BM309171
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|13790786|gb|BG653377.1|BG653377
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|208326000|gb|GE121026.1|GE121026
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|7232756|gb|AW568109.1|AW568109
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|193377081|gb|FK342718.1|FK342718
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
EST: gi|207710944|gb|GD694008.1|GD694008
EST:     GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTACTGCAGACACAAAG                         GCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA
genomic: GATCTCTAGTTGCAGAGCCTGTTGCAACTCCCCCTGCTGCAGACACAAAGgcaagtgttt ... tgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcttaactcaaatggttggttgatctttgactgaatgcaacctgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAAGAGACAGAAGAAGAGAAGAAGGCAGCAGAGGAACGGGCAGCTGCAGTGA
                                           cctgttcttc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtgttttcctaatggtttcatgttttcttttcactttgtgtgtcttaactcaaatggttggttgatctttgactgaatgcaacctgttcttcagGCTGCTGTTGCTGAGGATGACGATGATGATGATGTGGATTTGTTCGGTGAAGAGACAGAAGAAGAGAAGAAGGCAGCAGAGGAACGGGCAGCTGCAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG