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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGTGCTGCTGCATTAGTGCTAGTGAGTGAAGAGAAGGCACGTGAGCTTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgctttgacaagttaatgttaacatgttttggtcttgattaatattattagcatttagagctaaagcagcagtgttttgcag

Basic information

species Glycine max
transcript GLYMA07G39870.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39870.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv18s0089g00560.t01 (Vitis vinifera), 5'ss of exon 3
TGATGGTGCTGCTGCATTAGTGCTAGTGAGTGAAGAGAAGGCACGTGAGCTTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgct-ttgacaagttaatgttaacatgttttggtcttgattaatattattagc-atttagagctaaagcagcagtgttttg--cag
||||||||| ||||||||||||||||||||||   ||||||||  ||||||| || | || || ||||| |||||   ||||||||| ||||| ||| |||| || || | |||||||  |  |  ||| | | ||||||| |  |  |      | ||    ||||| ||  | ||  |||  |||
TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCTTAGACTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAGgtactgttaaaaagttaacttatatctgtctcgatcttgat-acgaccacagatgacttgatactaaaacatgattggcttgggcag

upper sequence: GLYMA07G39870.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 9
TGATGGTGCTGCTGCATTAGTGCTAGTGAGTGAAGAGAAGGCACGTGAGCTTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgct-ttgacaagttaatgttaacatgttttggtcttgattaatattattagc-atttagagctaaagcagcagtgttttg--cag
||||||||| ||||||||||||||||||||||   ||||||||  ||||||| || | || || ||||| |||||   ||||||||| ||||| ||| |||| || |||| |||||||  |  |   |||| | ||||||| |  |  |      | ||    ||||| ||  | ||  |||  |||
TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCTTAGACTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAGgtactgttgaaaagttaacttatatcggtttcgatcttgat-atgaccacagatgacttgatactaaaacatgattggcttgggcag

upper sequence: GLYMA07G39870.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv18s0089g00590.t01 (Vitis vinifera), 5'ss of exon 5
TGATGGTGCTGCTGCATTAGTGCTAGTGAGTGAAGAGAAGGCACGTGAGCTTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgct-ttgacaagttaatgttaacatgttttggtcttgattaatattattagc-atttagagctaaagcagcagtgttttg--cag
||||||||| ||||||||||||||||||| ||   ||||||||  ||||||| || | || || ||||| |||||   ||||||||| ||||| ||| |||| || || | |||||||  |  |  ||| | | ||||||| |  |  |      | ||    ||||| ||  | ||  |||  |||
TGATGGTGCGGCTGCATTAGTGCTAGTGACTGGTAAGAAGGCAGTTGAGCTTAGAGTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAGgtactgttaaaaagttaacttatatttgtctcgatcttgat-atgaccacagatgacttgatactaaaacatgattggcttgggcag

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|19347386|gb|BM892266.1|BM892266
EST:     TTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAG                         GCGCCTGAATTATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATA
genomic: TTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgctttgac ... tgttttgcagGCGCCTGAATTATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATA
EST: gi|27427305|gb|CA938825.1|CA938825
EST:     TTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAG                         GCGCCTGAATTATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATA
genomic: TTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgctttgac ... tgttttgcagGCGCCTGAATTATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATA
EST: gi|19347062|gb|BM891942.1|BM891942
EST:     TTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAG                         GCGCCTGAATTATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATA
genomic: TTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgctttgac ... tgttttgcagGCGCCTGAATTATTTACAACTGCTCCTTCCCTTGCAATACCAAAAGCTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGTGCTGCTGCATTAGTGCTAGTGAGTGAAGAGAAGGCACGTGAGCTTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAGgtgctttgacaagttaatgttaacatgttttggtcttgattaatattattagcatttagagctaaagcagcagtgttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT