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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatctagctctattgcagtttcaatggttggtttttgtagtataattcaaggtttattgttactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG

Basic information

species Glycine max
transcript GLYMA15G06020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g41480.1 (Oryza sativa), 3'ss of exon 4
---aagatctagctctattgcagtttcaatggttggtttttgtagtataattcaaggtttattgttactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
    |||  |  | | |||   | ||  |||      |    || || |  | ||  |||    | | |||    |  |   | | ||| |  |  |    ||   ||||||||||| ||||| ||||| ||||| ||||| ||||||||||| |||||| ||||  | |||||||||||||||||||| ||||| ||  |||
cctgagactt--caccattcatggtttgatgaacaactgacttattacacatgaatatttgacat-attgacaccatttgtgtttattcttgtacatgtgcagTGCGAGCTGAGGGCTTTCTTCGATGTCCATGAGCAAGAGGGAAGCTACCCTGGAGGGATTCACCTGGAGATGACAGGGCAGAACGTTACAGAGTGCATTG

upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g37790.1 (Oryza sativa), 3'ss of exon 4
aagatctagctctattgcagtttcaatggttggtt--tttg----tagtataattcaaggtttattgttactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
   |||   | |  ||  | ||  | |      ||  ||||    ||  || |     |  |||     ||| | ||| | || |||| | ||||  ||     |||||||| || | ||||||||||||||||| || |||||||| ||| ||||||||||||| ||| | |||||||| || || || |||||||||||  | |
---atcgtacacgtttaaacttctactatactattcatttgacattaacatgaccggcgacttaaatcaactaa-gatgactt-atgt-tgccttcttgaaaccagGCTGAGGTGCGCGCATTCTTTGATGTGCACGAACAAGAAGGCAGCCACCCAGGAGGGGTGCATCTGGAGATGACTGGACAAAATGTGACAGAATGCATCG

upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G155813_T01 (Zea mays), 3'ss of exon 3
aagatctagctctattgcagtttcaatggttggtttttgta-gtataattcaaggttt---attg-----ttactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
       |  |||| || ||| |  |   ||| | |  | |  |   ||||  |  ||   | |      ||||   || |  | ||  |   ||| |     | |||||||||  || | |||||||| || ||||||||||||||||||||  ||||||||||  | ||  | || ||||| |||||||||||||| || ||  |||
-------atttctactggagtgtttacacttgatctaggaacattccattctggccttccaactaataccttaccattgctctaatcgcgaactccatatc--taatagGCTGAAGTGCGTGCATTCTTCGACGTGCATGATCAAGAAGGAAGTCACCCAGGAGGCATCCACCTTGAAATGACTGGGCAGAACGTGACCGAGTGCATTG

upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G389336_T01 (Zea mays), 3'ss of exon 5
aagatctagctctattgcagtttcaatggttggttt-------ttgtagtataattcaaggtttattgt--tactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
       |  |||| || ||| |  |   ||| | |       ||  | |||           || |    |||   || |  | ||  |   ||| |     | | |||||||  || | |||||||| || ||||||||||||||||||||  ||||||||||  | ||  |  | ||||| |||||||||||||| || ||  |||
-------atttctactggagtgtttacacttgatctaggaacattccattatggccttccaactaataccataccattgctctaatcgcgaactccatatc--taacagGCTGAAGTGCGCGCATTCTTCGACGTGCATGATCAAGAAGGAAGTCACCCAGGAGGCATCCACCTTAAAATGACTGGGCAGAACGTGACCGAGTGCATTG

upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G454719_T01 (Zea mays), 3'ss of exon 6
aagatctagctctattgcagtttcaatggttggtttttgta-gtataattcaaggttt---attgttactg-atgataaattca--tgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
       |  |||| |  ||| |  |   ||| | |  | |  |   ||||  |  ||   | || |||   |  ||   |  |   | |  |        | | |||||||  || | |||||||| ||  |||||||||||||||||||  ||||||||||  | ||  | || ||||| |||||||||||||| || ||  |||
-------atttctactagagtgtttacacttgatctaggaacattccattctggccttccaactgataccacaccattgctctaatcgcgaactccatatctaacagGCTGAAGTGCGCGCATTCTTCGACATGCATGATCAAGAAGGAAGTCACCCAGGAGGCATCCACCTTGAAATGACTGGGCAGAACGTGACCGAGTGCATTG

upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G33510.1 (Arabidopsis thaliana), 3'ss of exon 4
aagatctagctctattgcagtttcaatggttggtttttgtagtataattcaaggtttattgttactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
   |||   |    || |   ||||        | |   || | |   | | | || || ||   |    || || | || || |   |         |||| ||  |||| || ||||| || || |||||||||||||| || | ||| || |||||||||||||| ||||| || || ||||||||||||||||| |
gtaatcattcgaacttacttcttcatccaactctatgcataatcttgcttatgattcat-gtagttacccattaaattatatggtgtat--------cagGCGGAATTGAGAGCGTTCTTCGACGTCCATGATCAAGAAGGGAGTTTCCCTGGCGGGGTTCATTTAGAAATGACTGGTCAAAACGTGACAGAATGTGTCG

upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1217g00010.t01 (Vitis vinifera), 3'ss of exon 4
----aagatctagctctattgc----agtttcaatggtt--ggtttttgtagtataattcaaggtttattgt---tactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
     |  | || |  |   ||    | ||||||   |   || | ||||      ||  |  | ||||| |      ||  |||  ||| | ||| |  |   | ||   || | ||  || | || ||||||||||| |||||||||||||| ||| |||||||||| |||||| | || ||||| |||||||| || ||||| ||  |||
gtaagaactttaccaatgaagccaagattttcaaacttccaggatcttgtcaatccatagattggttattttacactttggggattcattgaggtgcttttctctcttt-cagTCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCAGGAGGAGTTCATCTGGAAATGACTGGGCAGAATGTAACAGAGTGCATTG

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|6916081|gb|AW397611.1|AW397611
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|8825878|gb|BE209608.1|BE209608
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|37997399|gb|CF808988.1|CF808988
EST:     TCTTTTGATGCATTAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: TCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|192329375|gb|FK021829.1|FK021829
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGTATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|120495643|gb|EH223810.1|EH223810
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|19346052|gb|BM890932.1|BM890932
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|7796655|gb|AW782052.1|AW782052
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|6915150|gb|AW396611.1|AW396611
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|22524982|gb|BU083793.1|BU083793
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|9819280|gb|BE554793.1|BE554793
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|192329376|gb|FK021830.1|FK021830
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGTATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|298190989|gb|HO038468.1|HO038468
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTCGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|23729083|gb|BU762626.1|BU762626
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|308098317|gb|HO760058.1|HO760058
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|298190637|gb|HO032758.1|HO032758
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|10709234|gb|BF008958.1|BF008958
EST:     CCATTAAAGCTCCATCTGGACTTAGAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|11412990|gb|BF425001.1|BF425001
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGATGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|105633416|gb|DW246779.1|DW246779
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|151401351|gb|EV271165.1|EV271165
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|209698159|gb|BW661104.1|BW661104
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|23059224|gb|BU578362.1|BU578362
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
EST: gi|6846947|gb|AW349237.1|AW349237
EST:     CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGG                         GCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA
genomic: CCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttca ... atgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcaaggtttattgttactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG
         tttattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatctagctctattgcagtttcaatggttggtttttgtagtataattcaaggtttattgttactgatgataaattcatgtgttccttgatgttgatagGCTGAGCTGAGGGCATTCTTTGATGTGCATGATCAAGAAGGAAGCTACCCAGGAGGGGTTCATTTAGAGATGACAGGGCAGAACGTGACAGAATGTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - -tgcagtt
- - - - - - - - - - - - - tggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatg