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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcctagccctgcgcatacagttttttcttcctttttgtttaattattttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAATAGATATCAACGCCAAAGACTTTATACTCGTATTGCAT

Basic information

species Glycine max
transcript GLYMA10G44190.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g05660.1 (Oryza sativa), 3'ss of exon 6
gttagtttcctagccctgcgcatacagttttttcttcctttttgtttaattattttgtgtaactattgtttgtctcaataat-gcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAATAGATATCAACGCCAAAGACTTTATACTCGTATTGCAT--------
                   | || || |||||| |   |      |  | | |      | | | |   |   ||  ||| |      |||||||| ||  | || |||||    ||||| || ||||||||  | || ||| | ||||| || |||||||||||||||||||| |||||||| ||||| |        
-------------------gtatgcaattttttttctttccactatatactgtacataatgaatgtgcataacctgtatacttattcacagagaggcgtcgagctgtttctgtgctgggccataatgcaaggtttcgccatgatgttgcagAACAGATATCAACGCCAAAGACTATATACTCGGATTGCTTTAGGAAAG

upper sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G10430.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtttcctagccctgcgcatacagttttttcttcctttttgtttaattatttt--gtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAATAGATATCAACGCCAAAGACTTTATACTCGTATTGCAT
            |   |||  | ||   | | | ||  |      | ||   ||      |||| |||| | | |  |   ||| | |||||||||| || || ||||| ||||| ||||||||||||||||| || || |||||||| ||||| |||||||||||||||||| | || ||||| |||||| 
------------gtaatgcttagacttatatctgtttatgaagactaaaaagttcacaaagtaaatattatatatgacttcaattc-tgcagAGAGGAGTCCATCTTTTCCTACAATGGGCTATGATGCAAGGTGTCGCCATGCTTTTACAAAACAGATATCAACGCCAAAGATTATACACTCGCATTGCAC

upper sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 5
lower sequence: AT1G33230.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtttcctagccctgcgcatacagttttt-tcttcctttttgtttaa---ttattttgtgta-actattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAATAGATATCAACGCCAAAGACTTTATACTCGTATTGCAT
            |   || | ||  | || || || | | |   |  |||    |||       |   ||| | || |   ||   |   |||||| ||| || |  ||||| || || ||||||||||||||||| || || |||||| |||||||||||||||| ||||||||| | || ||||| |||||| 
------------gtattgggtattaacttattatcatacatgcagagtaaaatctatccaacaaatgttatagattattctaaatctat-tgcagAAAGGAGTGCGTCTTTTCCTCCAATGGGCTATGATGCAAGGTGTCGCGATGCTTCTGCAAAATAGATATCAGCGCCAAAGATTATACACTCGCATTGCAC

upper sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 3'ss of exon 6
gttagtttcctagccctgcgcatacagttttttcttcctttttgtttaattattttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAATAGATATCAACGCCAAAGACTTTATACTCGTATTGCAT
    ||| |   ||  | |   || |  ||  | |   ||||| | || ||||||  |   || |||       | |||  ||  |||||||||| ||||||||||| ||||| ||||||||||||||||||||||| |||||  | |||||||||||||||||||| |||||||||||||| |||||||
----gttact--gcatttccattataaattgat-taaatttttttatatttatttgataggaccatt-------taaatcttg--tgcagAGAGGGGTACAACTTTTCCTACAATGGGCTATGATGCAAGGAGTTGCTATGCTACTACAAAATAGATATCAACGCCAGAGACTTTATACTCGCATTGCAT

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|209697541|gb|BW670042.1|BW670042
EST:     GTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: GTGCAAAAAAGCAGgttagtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
EST: gi|58021387|gb|CX708128.1|CX708128
EST:     TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAGgttagtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
EST: gi|58024474|gb|CX711215.1|CX711215
EST:     TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAGgttagtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
EST: gi|298189043|gb|HO035680.1|HO035680
EST:     TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAGgttagtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
EST: gi|23727946|gb|BU762014.1|BU762014
EST:     GAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCNNNNNNNGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAAT
genomic: GAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAA-GCAGgttagtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAAT
EST: gi|254346987|gb|GR857191.1|GR857191
EST:     TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAGgttagtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttttgtttaattattttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAATAGATATCAACGCCAAAGACTTTATACTCGTATTGCAT
                     gtgtaac  putative branch site (score: 3)
     tttgtttaattatttt  TA-rich tract