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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtactcaactacatttttttattgctcaaatttctaggaagataatgattgatttcttatgatgtgaatgctttctgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT

Basic information

species Glycine max
transcript GLYMA10G41920.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 12
gcaagtact-caactacatttt--tttattgctcaaatttctaggaagataatgattgatttcttatgatgtgaatgctttctgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
| ||| | | |||||  ||| |  |||  |  || | || ||   ||    |  | | |     |  ||||   || |            |||| || || || || |||||||| || || ||||| ||||||||||| ||||| ||||| || ||||| ||||||||||| ||||| || |||||||| 
gtaagcaatgcaactgaattgtgttttgcttgtctatttcctgataaatacacaactcacactct--gatgaccatac------------agTTCACTCCTCATCCACATGCTGGTGATAAGTGGTGCATCTATCCAAGCTATGACTATGCTCACTGCATGGTGGATTCTCTTGAGAACATTACACATTCG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 12
gcaagtactcaactacatttttttattgctcaaatttctaggaag-ataatgattgatttcttatgatgtgaatgctttctgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
| ||  | |   | ||||| |    || ||    |||||  ||||  ||    || || | ||   || |        ||| ||    ||||||| || || || |||||||| ||||| |||| |||||||||||| ||||| ||||| |||||  | || || ||||| || || || || ||||| 
gtaaacaatt--cgacattatggagttact--gttttctgtgaagtgtagaatttaatatatttctatata-------tctacac---agTTTACACCTCATCCCCATGCTGGCGACAAGTGGTTTATCTATCCAAGCTATGACTATGCTCATTGTTTGGTTGACTCTCTTGAAAACATTACCCATTCG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 11
gcaagtactcaactacatttttttattgctcaaatttctaggaagataatgattgatttcttatgatgtgaatgctttctgcat-tttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
    |||    ||     |    |  |  | || ||||     | ||||     ||  |           |||  ||| ||||  |  |||| ||||| || || |||||||| || || |||||||||||||| || ||||| ||||| |||||||| ||||||||||| || || ||||| ||||| 
----gtaagtgacattgctcaactgattattaattttcacaatatataacatcagaact-----------aattgtttatgcacatacagTTCACCCCTCATCCACATGCTGGTGATAATTGGTGTATCTATCCGAGCTATGACTATGCTCATTGCATGGTGGATTCTCTTGAAAACATCACGCATTCG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
gcaagtactcaactacatttttttattgctcaaatttctaggaagataatgattgatttcttatgatgtgaatgctttctgcat-tttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
    |||    ||     |    |  |  || ||||||  |  | ||||     ||  |           |||  ||| | ||  |  |||| ||||| || || |||||||| ||||| |||||| ||||||| || ||||| || || |||||||| ||||||||||| || || ||||||||||| 
----gtaagtgacagtgctcaactgataatctaatttcatgatatataacatcagaact-----------aattgtttatacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
gcaagtactcaactacatttttttattgctcaaatttctaggaagataatgattgatttcttatgatgtgaatgctt--tctgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
||||||    ||||| | |  | | | | |  |  |   | | ||    |   |  | | ||    | ||| |  ||  | ||| ||  ||||  | || || ||| | ||||| ||||| |||||||||||||| |||||||||||||| || |||| ||| |||||||| |||||||| || ||||| 
gcaagtga--aactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------gcaagtactcaactacatttttttattgctcaaatttctaggaagataatgat-tgatttcttatgatgtgaatgc-tttctgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
                         || || |  |  |    |  ||| |     |  |   |  || | ||  |  ||| |  |||  |  ||| | |  ||||    |  ||||||| || ||||| |||||||||||||| |||||| | ||||||||||| |||||||| ||||||||||| |||||||| ||||| ||||| ||||| 
gcaagtctgtactcatagacatcttaactatttcaacatgagtagttactaaattacctatcaaaaaaaaaaaaacatgagtagttactaattgatttcacttcttttgtccagTTTACTCCTCACCCACATGCTGGAGACAAGTGGTGTGTTTATCCAAGTTACGATTATGCTCATTGCATTGTAGATTCTCTTGAGAACATCACTCATTCA

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 13
gcaagtactcaactac-atttttttattgctcaaatttctaggaagataatgattgatttcttatgatgtga-atgctttctgcat-tttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
|||||| || | ||   |   | || | ||||| |||      ||| || |  |   | |   | | | ||| ||  ||  |     |  |||||||||| || || ||| | || ||||| |||||||| |||||||||||||||||| | |||||||||||||||||||| || ||||| |||||||| 
gcaagtgctaacctttgaacatgttgtagctcacattc-----aaggtactactctttattcaagggtttgacatttttgttattcgtccagTTTACCCCTCATCCACATTCAGGGGACAAGTGGTGTATTTATCCAAGTTATGATTATTCTCATTGCATTGTGGATTCTCTTGAAAATATTACACATTCG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
lower sequence: PP1S43_166V6.1 (Physcomitrella patens), 3'ss of exon 14
-gcaagtactcaact-acatttttttattgctcaaatttctaggaagataatgattgatttctta-tgatgtgaatgct----ttctgcatttt-----agTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
 | ||||  ||| || | |  ||  |      |  || | |     | | |||||    |   |  |||   | |  ||    ||    | | |     ||||||| || ||||| |||| |||||| ||||||||||| ||||| || || |||||  | ||||||||||| ||| || | |||||  | || ||||| 
tggaagt-ttcatctgaaacattgctgccatccggatctgtgttttggtcatgatgatctctgtgctgacaagtacactgtggtttcaaactcttgtgcagTTTACTCCTCACCCACATGTTGGAGATAAATGGTGTATATATCCTAGCTACGATTACACGCATTGCATTGTTGATGCTTTGGAGAACGTTACCCATTCA

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|31561586|gb|CD487424.1|CD487424
EST:     TGCAGAGTGATAACTACAATATGTATGACCTTATTGCATATAGAATTAAG                         TTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTAT
genomic: TGCAGAGTGATAACTACAATATGTATGACCTTATTGCATATAGAATTAAGgcaagtactc ... tgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTAT
EST: gi|254327577|gb|GR837186.1|GR837186
EST:     TGCAGAGTGATAACTACAATATGTATGACCTTATTGCATATAGAATTAAG                         TTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTAT
genomic: TGCAGAGTGATAACTACAATATGTATGACCTTATTGCATATAGAATTAAGgcaagtactc ... tgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctaggaagataatgattgatttcttatgatgtgaatgctttctgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT
                gattgat  putative branch site (score: 4)
                                      tgctttct  putative PPT
           ataatgattgattt  TA-rich tract