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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatctgttatgatgcttggattttcttggttgtgttcatgcttacaagttaacatcattttgtgtatagattcttacatcttttcttctaacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTGAATTT

Basic information

species Glycine max
transcript GLYMA0048S00290.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.3 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 9
--acatctgtta-tgatgcttggattttcttggttgtgttcatg--cttacaagttaacatcattttgtgtatagattcttacatcttttcttctaa----caggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTGAATTT
   | | ||  | |  ||||  ||  |   || ||   ||||||  ||   | | |  || |    ||  | |    | ||| ||| ||| |   ||    ||||||||||| || ||||| ||||| || ||||||||||| ||||||||| |||| || ||||| |  |||||||||||| | | | || ||   ||          
cttcttttgcaaatactgctgtgaagtatctgatttgtttcatgagctctaaggctcgcagc----tgattctgatcttttatatcctttgtctaaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGAGGACCGAGGACTGCTGTCCCATATTTCCTCTGACTTCATCAATTGTACA-----

upper sequence: GLYMA0048S00290.3 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G518717_T03 (Zea mays), 3'ss of exon 5
acatctgttatgatgcttg--gattttcttggttgtgttcatgcttacaagttaacatcattttgtgtatagattcttacatctttt---cttctaacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTGAATTT
  |   ||| | || |     | |||     ||||  |  | |  |   |    | ||      |    |   ||   | || ||||   ||  |||||||||||||| || || || ||||| || |||||||| |||||||||||| ||||||| ||||| |  |||||||||||| | | | || |  | |   ||      
caacaagtttttattccaactgctttctgaagttgcctagaagtgtttcatgagatatatgaccgatgctgatttacaatatgttttaatctgttaacagGAAAGAGATGTCAAGTTCTTCACAGAGACAGAGGAAAACAACCAGATGCGAGGCCCAAGGACTGCAGTCCCATATTTCCTCTGACTTCAATTGTACATTT-----

upper sequence: GLYMA0048S00290.3 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G055905_T01 (Zea mays), 3'ss of exon 9
-acatctgttatgatgcttggattttcttggttg--tgttcatgctt-acaagttaacatcattttgtgtatagattcttacatctttt---cttctaacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTGAATTT
   |   ||| ||   |   | |||     ||||  |  | ||| || |  || ||  || | ||  ||      ||   | || ||||   ||  || |||||||| || || || || ||||| || ||||||||||||||||||||| ||||||| ||||| |  |||||||||||| ||| | || |     || |  |||| 
ccaacaagttttgtcccactgctttctcaagttgcctactaatgtttcatgagata-tatgacttgatgc-cgacttacaatatgttttgcactgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGAGGCCCAAGGACCGCAGTCCCATATTTCCTATGACTTCAA----TTGTACAATT-

upper sequence: GLYMA0048S00290.3 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 9
acatctgttatgatgcttggattt------tcttggttgtgtt-catgcttacaa-gttaacatcattttgtgtatagattcttacatcttttcttctaacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTGAATTT
  || | |||| || ||   | ||      | ||  ||| |||  |   |||    |||   ||  | |   ||||  ||| | | || |||||  ||  ||||||||||| || || |||||||| ||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||| |  |          ||    
-tatttattattattctataaattagctggtgttaattgggttatacctttattgtgttggaatggtgtatggtattcattatca-atattttccactt-cagGAAAGAGAGGTGAAGTTTTTCACAGAAACAGAGGAGAACAACCAGATGAGAGGGCCAAGGACAGGAGTCCCATATTTCTTATAAGTGAAAAAAAG---GGAGC--

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|209728925|gb|BW651715.1|BW651715
EST:     TTAGTTTCAATGAAAATATG                         AGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCC
genomic: TTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCC
EST: gi|254337376|gb|GR849329.1|GR849329
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|254337376|gb|GR849329.1|GR849329
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|209728248|gb|BW651683.1|BW651683
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         AGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCC
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCC
EST: gi|207746865|gb|GD721124.1|GD721124
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGGAAAG                     
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATAT-----Ggtgagccacc ... aacagg
EST: gi|213611336|gb|DB983956.1|DB983956
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGGAAAG                     
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATAT-----Ggtgagccacc ... aacagg
EST: gi|213593175|gb|DB975366.1|DB975366
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|213593175|gb|DB975366.1|DB975366
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|5753202|gb|AI960489.1|AI960489
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         AAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaagA---GA-A-GTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|31473271|gb|CD415284.1|CD415284
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGGAAAG                     
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATAT-----Ggtgagccacc ... aacagg
EST: gi|254340656|gb|GR854384.1|GR854384
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-
EST: gi|254340656|gb|GR854384.1|GR854384
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         G
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... aacaggaaag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttaacatcattttgtgtatagattcttacatcttttcttctaacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTGAATTT
                                         ttctaac  putative branch site (score: 1)
                                catcttttcttcta  CT-rich tract
         atcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatctgttatgatgcttggattttcttggttgtgttcatgcttacaagttaacatcattttgtgtatagattcttacatcttttcttctaacaggaaagAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTGAATTT

-catctgt
- - - - - tgatgct
- - - - - - - - - - - - - - ggttgtg
- - - - - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg