Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcaacatctgttatgatgcttggattttcttggttgtgttcatgcttacaagttaacatcattttgtgtatagattcttacatcttttcttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTG

Basic information

species Glycine max
transcript GLYMA0048S00290.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 9
tggcaacatctgtta-tgatgcttggattttcttggttgtgttcatg--cttacaagttaacatcattttgtgtatagattcttacatcttttcttctaa----cagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTG
   |  | | ||  | |  ||||  ||  |   || ||   ||||||  ||   | | |  || |    ||  | |    | ||| ||| ||| |   ||    ||||||||||| || ||||| ||||| || ||||||||||| ||||||||| |||| || ||||| |  |||||||||||| | | | || ||   ||     
---cttcttttgcaaatactgctgtgaagtatctgatttgtttcatgagctctaaggctcgcagc----tgattctgatcttttatatcctttgtctaaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGAGGACCGAGGACTGCTGTCCCATATTTCCTCTGACTTCATCAATTGTACA

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G518717_T03 (Zea mays), 3'ss of exon 5
tggcaacat-ctgttatgatgcttggattttcttggttgtgttcatgcttacaagttaacatcattttgtgtatagattcttacatctttt---cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTG
   |||||   | ||||      ||  |||     ||||  |  | |  |   |    | ||      |    |   ||   | || ||||   ||  |||||||||||||| || || || ||||| || |||||||| |||||||||||| ||||||| ||||| |  |||||||||||| | | | || |  | |   || 
---caacaagtttttattccaactgc-tttctgaagttgcctagaagtgtttcatgagatatatgaccgatgctgatttacaatatgttttaatctgttaacagGAAAGAGATGTCAAGTTCTTCACAGAGACAGAGGAAAACAACCAGATGCGAGGCCCAAGGACTGCAGTCCCATATTTCCTCTGACTTCAATTGTACATTT

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G055905_T01 (Zea mays), 3'ss of exon 9
tggcaacatctgttatgatgcttggattttcttggttg--tgttcatgctt-acaagttaacatcattttgtgtatagattcttacatctttt---cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTG
   |||||  | || |    ||  | |||     ||||  |  | ||| || |  || ||  || | ||  ||      ||   | || ||||   ||  || |||||||| || || || || ||||| || ||||||||||||||||||||| ||||||| ||||| |  |||||||||||| ||| | || |  | |    | 
--ccaacaagttttgtcccact--gctttctcaagttgcctactaatgtttcatgagata-tatgacttgatgc-cgacttacaatatgttttgcactgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGAGGCCCAAGGACCGCAGTCCCATATTTCCTATGACTTCAATTGTACAATT

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 9
tggcaacatctgttatgatgcttggattttcttggttgtgtt-catgcttacaa-gttaacatcattttgtgtatagattcttacatcttttcttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTG
|    |    | || |     || | |  | ||  ||| |||  |   |||    |||   ||  | |   ||||  ||| | | || |||||  ||  ||||||||||| || || |||||||| ||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||| |  |           
tatttattattattctataaattagctggtgttaattgggttatacctttattgtgttggaatggtgtatggtattcattatca-atattttccactt-cagGAAAGAGAGGTGAAGTTTTTCACAGAAACAGAGGAGAACAACCAGATGAGAGGGCCAAGGACAGGAGTCCCATATTTCTTATAAGTGAAAAAAAGGGAGC

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|254340656|gb|GR854384.1|GR854384
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGG
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGG
EST: gi|213611336|gb|DB983956.1|DB983956
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|209728925|gb|BW651715.1|BW651715
EST:     TTAGTTTCAATGAAAATAT-                         ----GAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: TTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|193346878|gb|FK310146.1|FK310146
EST:     TTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACA
genomic: TTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAA-TATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACA
EST: gi|207746865|gb|GD721124.1|GD721124
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|31464149|gb|CD406177.1|CD406177
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGTATGAG
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAG-ATGAG
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|209728248|gb|BW651683.1|BW651683
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATAT-                         ----GAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|213593175|gb|DB975366.1|DB975366
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|207791752|gb|GD763659.1|GD763659
EST:     TTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: TTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|31473271|gb|CD415284.1|CD415284
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|254337376|gb|GR849329.1|GR849329
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|5753202|gb|AI960489.1|AI960489
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         AAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttacaagttaacatcattttgtgtatagattcttacatcttttcttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGAGGCCCCAGGACAGGCGTCCCATATTTCTTATAAATTGATGTTTTTCTTG
                               ttcttac  putative branch site (score: 2)
                               ttcttacatcttttct  CT-rich tract
              atcatttt  TA-rich tract