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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatctatttcttttgaaaatttaagattttgatgttgtttcattcttttaattaactattttcttgaggtagtttaatcaagtgagaagatcaat...

Basic information

species Glycine max
transcript GLYMA0048S00290.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 8
TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatctattt--------cttttgaaaatt-taagattttgatgttgtttcattcttttaattaa--ctattttcttgaggtagtttaatcaagtgagaagatcaat----
|||||  | || |||||||| ||||| ||||| || || ||||| || ||||| |||||  | ||||| ||||| ||||| ||||||||||||||||||||| ||| ||          |   || |||  ||  ||| |  |    ||  |||  |||  | ||  || || | |||| |       | |  |  | |   |   |    
TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattgatgctcacataccctgcaataccttttttccag

upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 8
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 8
TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatcta--tttcttttgaaaatttaagattttgatgttgtttcattcttttaattaactattttct-tgaggtagtttaatcaagtgagaagatcaat
|| ||  | || |||||||||||||| || ||||| || ||||| || || ||||||||||| ||||| |||||||| |||||||| |||||||||||||||  ||   || ||| |||  ||||  |||  |   |  || | ||    ||  | |  | | |||| |    |  |||  | |||             
TTTAACCATATTAACAATCTTGATCTAGTATGTCGCGCTCACCAGCTTGTACAAGAAGGTCTCAAGTACATGTTCCAAGATAAAGGTCTTGTAACTgtaagtgccttgcttccttatgatcattttggatagttg-gaagtataatctgcttggtgatgtttcttctctttattttttttgtaaag-------------

upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 8
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 8
TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatctatttcttttgaaaatttaagattttgatgttgtttcattcttttaattaactattttcttgaggtagtttaatcaagtgagaagatcaat
|| ||  | || ||||| || ||||| || || || || |||||||| || ||||||||||||||||| |||||||| |||||||||||||||||||| ||| ||   | ||| | |  | || | |||||  | ||  |      ||| ||       ||       | || |||  |   ||  |   |     
TTTAACCATATCAACAAGCTGGATCTAGTATGCCGCGCGCACCAACTTGTACAAGAAGGTCTTAAGTACATGTTCCAAGATAAAGGCCTTGTAACTgtgagtgtc--ctgcttctaatgaattgatattttt-tattagtgggcgttttgaaactctgcttagtgattgttaattttgttttgtttgtgaag----

upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 8
TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatctatttcttttgaaaatttaagattttgatgttgtttcattcttttaattaactattttcttgaggtagtttaatcaagtgagaagatcaat
|||||  |||||||||||||||||||||||||||| || ||||| || || ||||||||||| ||||| ||||| ||||||||||| || ||||| |||||  ||| |   ||||   | ||     |||||   | |    ||  ||||||  | | || ||       |||||| ||    |||     |||  
TTCAACCACATAAACAATCTTGATCTGGTTTGTCGAGCCCACCAGCTTGTACAAGAAGGTCTAAAGTACATGTTTCAGGATAAAGGACTCGTAACCgtaagattctgtagatttttgcagtt----gttttgtcatcg----atagttttaaccatcaatatt-----aatagtttgattct-tgactttttcag-

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|151410851|gb|EV280666.1|EV280666
EST:     TCGTTCAAGAAG-TCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|254337376|gb|GR849329.1|GR849329
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|209728248|gb|BW651683.1|BW651683
EST:     TCGTTCAAGAATGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|207746865|gb|GD721124.1|GD721124
EST:     CAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: CAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|213611336|gb|DB983956.1|DB983956
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|213593175|gb|DB975366.1|DB975366
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|5753202|gb|AI960489.1|AI960489
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|31473271|gb|CD415284.1|CD415284
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|254340656|gb|GR854384.1|GR854384
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatctatttcttttgaaaatttaagattttgatgttgtttcattcttttaattaactattttcttgaggtagtttaatcaagtgagaagatcaat

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG