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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttcctagccctgtgcatatagttttttcttccttttttatttttaatcatgttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAACAGATATCAACGCCAAAGACTCTATACTCGTATTGCAT

Basic information

species Glycine max
transcript GLYMA20G38960.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g05660.1 (Oryza sativa), 3'ss of exon 6
gttggtttcctagccctgtgcatatagttttttcttccttttttat-ttttaatcatgttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAACAGATATCAACGCCAAAGACTCTATACTCGTATTGCAT--------
                   | ||  | |||||| |   |    ||| |  |   |||  ||  |    ||    ||| | | | || ||  |||||||| ||  | || |||||    ||||| || ||||||||  | || ||| | ||||| ||||||||||||||||||||||| |||||||| ||||| |        
-------------------gtatgcaattttttttctttccactatatactgtacataatgaatgtgcataacctgtat-acttattca--cagagaggcgtcgagctgtttctgtgctgggccataatgcaaggtttcgccatgatgttgcagAACAGATATCAACGCCAAAGACTATATACTCGGATTGCTTTAGGAAAG

upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G10430.1 (Arabidopsis thaliana), 3'ss of exon 6
gttggtttcctagccctgtgcatatagttttttcttcctttttt-atttttaatcatgttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAACAGATATCAACGCCAAAGACTCTATACTCGTATTGCAT
                  ||| || | || | |||   | |    | |   ||         |||| |||| | | |  |   ||| | |||||||||| || || ||||| ||||| ||||||||||||||||| || || |||||||| |||||||||||||||||||||||| | || ||||| |||||| 
--------------gtaatgcttagacttatatctgtttatgaagactaaaaagttcacaaagtaaatattatatatgacttcaattc-tgcagAGAGGAGTCCATCTTTTCCTACAATGGGCTATGATGCAAGGTGTCGCCATGCTTTTACAAAACAGATATCAACGCCAAAGATTATACACTCGCATTGCAC

upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G33230.1 (Arabidopsis thaliana), 3'ss of exon 6
gttggtttcctagccctgtgcatatagttttttcttccttttttatttttaatcatgttgtgtaactattgt---ttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAACAGATATCAACGCCAAAGACTCTATACTCGTATTGCAT
            |   || | || ||  || || |      |  |   | ||   | |     || | || |   || |   ||   |   |||||| ||| || |  ||||| || || ||||||||||||||||| || || |||||| ||||||| |||||||| ||||||||| | || ||||| |||||| 
------------gtattgggtat-taacttattatcatacatgcagagtaaaatctatccaacaaatgttatagattattctaaatctat-tgcagAAAGGAGTGCGTCTTTTCCTCCAATGGGCTATGATGCAAGGTGTCGCGATGCTTCTGCAAAATAGATATCAGCGCCAAAGATTATACACTCGCATTGCAC

upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 3'ss of exon 6
gttggtttcctagccctgtgcatatagttttttcttccttttttatttttaatcatgttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAACAGATATCAACGCCAAAGACTCTATACTCGTATTGCAT
    ||| |   ||  |     ||||  ||  |     |||||||| |||| |       |   || |||       | |||  ||  |||||||||| ||||||||||| ||||| ||||||||||||||||||||||| |||||  | ||||| |||||||||||||| ||||| |||||||| |||||||
----gttact--gcatttccattataaattgattaaatttttttatatttatttg----ataggaccatt-------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|192319100|gb|FK010636.1|FK010636
EST:     GACTGTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: GACTGTGCAAAAAAGCAGgttggtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
EST: gi|192322148|gb|FK012252.1|FK012252
EST:     TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAGgttggtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG
EST: gi|22932228|gb|BU549367.1|BU549367
EST:     TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG                         AGAGGTGTACAACTTTTNNNACAGTGGGCTATGATGCAAGGAGTTGCAATG
genomic: TGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAGgttggtttcc ... atgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttatttttaatcatgttgtgtaactattgtttgtctcaataatgcatgcagAGAGGTGTACAACTTTTTCTACAGTGGGCTATGATGCAAGGAGTTGCAATGCTTTTGCAAAACAGATATCAACGCCAAAGACTCTATACTCGTATTGCAT
                     gtgtaac  putative branch site (score: 3)
     tatttttaatcatgtt  TA-rich tract