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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactctaattctgtaaatatatgcataagatattgtagacatctttatggttcttatactagattatggccttgatgtgcttctgttaaaatgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAGAAATGCTTGGAACAGTGGGCCCTCCTGTACCAAATGTGGATGTTTGCCT

Basic information

species Glycine max
transcript GLYMA01G43470.3
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.3 (Glycine max), 3'ss of exon 14
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 14
--------------------------------------------------------------------------------cactctaattct--gtaaatatatgcataagatattgtagacatctttatggttct---------tatactagattatggccttga---tgtgcttc-tgttaaaatgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAGAAATGCTTGGAACAGTGGGCCCTCCTGTACCAAATGTGGATGTTTGCCT
                                                                                |  |   |   |    ||| |||||   ||  | || |   | | | ||    | |           | ||| ||  ||   |||    | |  ||  | ||||  | ||  |||||||||||||||| |||||||| || ||||||||| | |||||||||||    |||||||| |||||||||||||| ||||||||||| || || |||||
gtatgcagtccattgaaattagtgtctacctgtcttatcctttttgactgtttctttgtgaagcattgaaattgaaatttcgttggcacctttgagaaacatatgtccaaagtttttttcccgtttctagtactgtgcaaagtagctttctacatggtgaatttggatctttattttgtattaatgttaatgtagGTCTGACTGAAACTTGTGCGGGCACATTTGTCTCACTGCCAAATGAAATTAGCATGCTTGGTACAGTGGGCCCTCCAGTACCAAATGTTGACGTATGCCT
















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|254347181|gb|GR856851.1|GR856851
EST:     GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATG                         GTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
genomic: GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATGgtatgctctt ... atgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
EST: gi|22525607|gb|BU084418.1|BU084418
EST:     GTGACTTGTGCTCATGTCCTACAGGGATATG                         GTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
genomic: GTGACTTGTGCTCATGTCCTACAGGGATATGgtatgctctt ... atgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
EST: gi|6666183|gb|AW277642.1|AW277642
EST:     GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATG                         GTCTGACTGANACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
genomic: GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATGgtatgctctt ... atgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
EST: gi|192295718|gb|FG990572.1|FG990572
EST:     GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATG                         GTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
genomic: GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATGgtatgctctt ... atgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
EST: gi|120533313|gb|EH261446.1|EH261446
EST:     GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATG                         GTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
genomic: GGAAGGTTACTTACGGGTGGTGACTTGTGCTCATGTCCTACAGGGATATGgtatgctctt ... atgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
EST: gi|22525677|gb|BU084488.1|BU084488
EST:     GTGACTTGTGCTCATGTCCTACAGGGATATG                         GTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG
genomic: GTGACTTGTGCTCATGTCCTACAGGGATATGgtatgctctt ... atgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggttcttatactagattatggccttgatgtgcttctgttaaaatgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAGAAATGCTTGGAACAGTGGGCCCTCCTGTACCAAATGTGGATGTTTGCCT
                        ccttgat  putative branch site (score: 5)
                                      tgttaaaatgaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactctaattctgtaaatatatgcataagatattgtagacatctttatggttcttatactagattatggccttgatgtgcttctgttaaaatgaaaatagGTCTGACTGAAACCTGTGCGGGAACCTTTGTCTCATTACCAAATGAAATAGAAATGCTTGGAACAGTGGGCCCTCCTGTACCAAATGTGGATGTTTGCCT

cactcta
- - - - ttctgta
- - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgatg