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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttctcttgttgatatccggtggtctacttttcatgtaacacaccaaatgacataccgaggatttttttagtaaaaaccaaaacttctaattttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGATTGTTAATCTCATCCGGAGCTCAAAGCTTGATGCCAAAATTGACTCCGAA

Basic information

species Glycine max
transcript GLYMA10G16090.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------------------------------------------------gcttctcttgttgatatc-cggtggtctacttttcatgt--aacacaccaaatgacataccgaggatttttttagtaaaaac-caaaacttctaatt---ttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGATTGTTAATCTCATCCGGAGCTCAAAGCTTGATGCCAAAATTGACTCCGAA
                                                                                          |    |   |  | ||  |  |   |  || || | ||  |  | |     ||   |   | || ||   || |||   |     | | | || ||   || |||| || |||||||| || || ||| |||| ||||||||||| |||||||||||||| || || ||||| | |||||||||||||||||| ||||| || || 
gtaagttctcacatttggttgtatatgtttacacataactctgctctccggattgctcaatgtttggaattttctctattccttatctttcccaacacatgaaaattgccatatccagctatttaagttgagaagaattgttgcggtcttgtggtttaactttgtactcatgtcgagcctatatttcccttgtcagGGTACTTGCTGAAAAATTGAATCTGAACTATGAGGAGGCCGAGAGATGGATTGTGAACCTAATCCGCACCTCAAAGCTTGATGCCAAGATTGATTCTGAG

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 6
gcttctcttgttgatatccggtggtctacttttcatgtaacacaccaa--atgacataccgaggattttttt---agtaaaaacca--aaacttctaatttttt-cagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGATTGTTAATCTCATCCGGAGCTCAAAGCTTGATGCCAAAATTGACTCCGAA
        || ||   |  ||   |  |     | |  |    |  |   |||| ||    |||  || ||    | ||    |        ||||    | |  |||||||||| |||| ||  | ||||||||||||||||| ||||| ||||||||||| ||||| ||   || ||||||||||||||| |||||||| ||  | 
--------tggtgggttttggcttttcaagcagcgttaatttgattagttatgaaattttaaggccttgttctcaactatgtgctgttggttttctggcatctggcagAGTGCTTTCTGACAAACTGAATTTGAATTATGAGGAAGCTGAAAGATGGATTGTGAATCTTATAACGACCTCAAAGCTTGATGCTAAAATTGATTCAAAG
















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|209703908|gb|BW661598.1|BW661598
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|192314055|gb|FK008795.1|FK008795
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAAGAGGCTGAGAAATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|58015713|gb|CX702455.1|CX702455
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|209696629|gb|BW666925.1|BW666925
EST:     ATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: ATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|193403478|gb|FK366848.1|FK366848
EST:     GCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: GCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|209697045|gb|BW667035.1|BW667035
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|209707122|gb|BW661576.1|BW661576
EST:     TCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: TCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|193434366|gb|FK401092.1|FK401092
EST:     GCATTGACATTGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGA
genomic: GCATTGACA-TGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGA
EST: gi|193392690|gb|FK359185.1|FK359185
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|31308156|gb|CD393359.1|CD393359
EST:     GAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: GAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|6481581|gb|AW200852.1|AW200852
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATCTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|11274645|gb|BF324982.1|BF324982
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|10254604|gb|BE822370.1|BE822370
EST:     CTATTTATNNTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|8283830|gb|BE021389.1|BE021389
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|7692748|gb|AW760848.1|AW760848
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|21600493|gb|BQ610824.1|BQ610824
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|254348332|gb|GR852011.1|GR852011
EST:     CTA-TTATC-TCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|58015407|gb|CX702149.1|CX702149
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|21479769|gb|BQ576452.1|BQ576452
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAG
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAG
EST: gi|193405196|gb|FK372573.1|FK372573
EST:     GCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: GCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|5761286|gb|AI966649.1|AI966649
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|12773923|gb|BG238850.1|BG238850
EST:     TACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTT-CTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: TACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
EST: gi|10709957|gb|BF009681.1|BF009681
EST:     CTATCTATCTTCGAGACATACTGTAGATTACACCGACGCATTGACATGTG                         AGTGCTTGGTGAGAAG
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAG
EST: gi|21888755|gb|BQ741968.1|BQ741968
EST:     CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGG                         AGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT
genomic: CTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcacct ... attttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatgacataccgaggatttttttagtaaaaaccaaaacttctaattttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGATTGTTAATCTCATCCGGAGCTCAAAGCTTGATGCCAAAATTGACTCCGAA
                                        ttctaat  putative branch site (score: 2)
                                       cttctaattttttc  CT-rich tract
                 atttttttagtaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttctcttgttgatatccggtggtctacttttcatgtaacacaccaaatgacataccgaggatttttttagtaaaaaccaaaacttctaattttttcagAGTGCTTGCTGAGAAGTTAAATTTGAATTATGAGGAGGCTGAGAGATGGATTGTTAATCTCATCCGGAGCTCAAAGCTTGATGCCAAAATTGACTCCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
gcttctc
- - - - tgttgat
- - - - - - - - - -ggtggtc
- - - - - - - - - - - - - - - - tcatgta
- - - - - - - - - - - - - - - - - - - -acacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - cataccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaac