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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcattttctacaataaaaatttgatggggttctttctgttttctacctttatctttaaagatccttatctttttacttgtcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAGAGCAAT

Basic information

species Glycine max
transcript GLYMA05G25780.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25780.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 3
gtcattttctacaataaaaatttgatggggttctttctgttttctacctttatc--tttaaagatccttatctttttacttgtcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAGAGCAAT
||  || |   | ||     |||  | |||     |  ||| |||| |  ||    |||    | | ||  | || |  ||   ||| |||||||| ||||  |||| || ||||||||| | ||||| |||||||| |||||||||||
gttgttata-gctatttgtttttcttagggaggaat--gttctctagccataatattttcttaaccattggcattgtgttt---attcgtagGTTTCTGACTTTGGAAGACTCTTTCTTGCTTGAAAACCGAGCAACCTTGAGAGCAAT
















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|193360313|gb|FK325111.1|FK325111
EST:     TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCG                         GTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
genomic: TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCGgtcattttct ... tcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
EST: gi|22524348|gb|BU083159.1|BU083159
EST:     TCAGCATCACCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCG                         GTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
genomic: TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCGgtcattttct ... tcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
EST: gi|207784324|gb|GD758971.1|GD758971
EST:     TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCG                         GTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
genomic: TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCGgtcattttct ... tcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
EST: gi|193477710|gb|FK439149.1|FK439149
EST:     TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCG                         GTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
genomic: TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCGgtcattttct ... tcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
EST: gi|193310780|gb|FK277560.1|FK277560
EST:     TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCG                         GTTTTTGACCATGG
genomic: TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCGgtcattttct ... tcatttgtagGTTTTTGACCATGG
EST: gi|207692007|gb|GD673924.1|GD673924
EST:     TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCG                         GTTTTTGACCA
genomic: TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCGgtcattttct ... tcatttgtagGTTTTTGACCA
EST: gi|193686673|gb|FK626080.1|FK626080
EST:     TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCG                         GTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG
genomic: TCAGCATCAGCAAAATTCCATCCACCATCTGTCAAATTGAATTTGATTCGgtcattttct ... tcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttttctacctttatctttaaagatccttatctttttacttgtcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAGAGCAAT
                                 tctttttacttgtc  CT-rich tract
             tttatctttaaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattttctacaataaaaatttgatggggttctttctgttttctacctttatctttaaagatccttatctttttacttgtcatttgtagGTTTTTGACCATGGATGATTCTTTCTTGTTAGAAAATCGAGCAACTTTGAGAGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA