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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag

Basic information

species Glycine max
transcript GLYMA17G34690.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os06g40940.3 (Oryza sativa), 5'ss of exon 11
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactgga-aaattattgtcctta------tgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag
||||||||||||  | |||||||| || || |||||||| || |||||||||||||| || |||||||| |||||||| |||||||| |||||||||||||||  ||  ||    | | | |||  ||||||      |     || || || | | | |  ||  ||| |  | | ||||     |                      
TGTTGCAAAGCGTTTGATGGACTATGGATTCCATGCACCTACTATGTCATGGCCTGTTCCAGGCACACTTATGATTGAACCAACTGAAAGTGAAAGCAAGgtaaaacactaaaacacatactatattccttagcattgtaccaaccattcttttatatgagcttaatgtcacatcaattatctcgcag---------------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os01g51410.2 (Oryza sativa), 5'ss of exon 11
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctta------ctggaaaatta-ttgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag
||||||||||||  | |||||||| || || |||||||| || |||||||||||||| || |||||||| |||||||| || ||||| |||||||||||||||  ||  ||      ||   | |||  ||| | || |     || || || | | | || ||  ||| |  | |||||||    |                      
TGTTGCAAAGCGTTTGATGGACTATGGATTCCATGCACCTACTATGTCATGGCCTGTTCCAGGCACACTTATGATTGAACCCACTGAAAGTGAAAGCAAGgtaaaacactaaaacacctactatattccttgccattgtaccaaccattcttttatatgaacttaatgtcacattatttatttcgcag---------------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G104310_T02 (Zea mays), 5'ss of exon 10
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag
||| ||||||||| | ||||||||||| || || ||||| || |||||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||||||  | | |         |||     ||| || | |||| || | |   | | ||  ||    |  |  |||   | |  | |   |     || | ||||
TGTGGCAAAGCGCTTGATGGACTACGGGTTCCACGCACCGACCATGTCATGGCCTGTTCCTGGCACACTTATGATTGAACCAACTGAAAGTGAGAGCAAGgta--agcatgtgcagcttttaaccatcttttgct-ccccgttctatgaattagttgatttcacatgagcttacaatatcgtaccgttt--tgtcttggcag

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: AT4G33010.2 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag
||| || || || || |||||||| || || |||| ||| |||||||| |||||||| ||||| || || |||||||||||||| ||||||||||||||||||      || |||| |  |   |  ||     || | |||| |  |   |        ||| |  || ||  |    || | ||  | |     ||||||
TGTGGCGAAACGGCTAATGGACTATGGATTCCATGGACCCACAATGTCTTGGCCTGTCCCTGGAACTCTTATGATTGAGCCAACCGAGAGTGAAAGCAAGgta----aata-tggatatatgcagatctctcattgactctttcttctctca--------gtgtatcaacttgatga--aactaaataatattcgtttgcag

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 12
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattcttta-attcaactaaacatcattgcag
||| || || ||  | ||||| || ||||| |||| ||| |||||||| |||||||| ||||| || || ||||| |||||||| || || |||||||||||| |    |  || |   ||    | |  ||    | |    |    | | | | | |     |    || ||  |||  ||  |  ||   |  ||| |||
TGTGGCCAAACGATTGATGGATTATGGTTTCCATGGACCGACAATGTCTTGGCCTGTCCCTGGAACGCTTATGATCGAGCCAACCGAAAGCGAAAGCAAGgtaattatgtcttgca---ttgcattgcaaatctctcactgactcagctctcagtctctaaaacatggcttcataatttgtatatatatatgtaatatttcag

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 5'ss of exon 12
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag
| |||| ||||| || |||||||| || ||||||| ||| |||||||||||||| |||||||| |||||||||||||| || ||||| ||||||||||||||||  | | ||  |  || |  |    || | ||       |     | |    || | ||||| |  |   |   ||  ||  |||   ||         
TATTGCTAAGCGTCTTATGGACTATGGATTTCATGGACCGACAATGTCATGGCCAGTGCCTGGTACACTCATGATTGAACCCACTGAAAGTGAAAGCAAGgtat-gcttcaccagggaaattcttcttttttcatcttttcatactcctttcttcttctagtgaattt-taagtgtgtttgttttacttttcag--------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 5'ss of exon 13
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag
|||||| || || |||||||| || || || ||||  ||||||||||| ||||| || || || |||||||||||||| || ||||| ||||||||||||||          |  || | ||   | ||  | ||  | | || | ||||| | |||   || ||   |||     || || |    |   ||         
TGTTGCTAAACGTCTCATGGATTATGGGTTCCATGGGCCAACAATGTCCTGGCCAGTACCAGGAACACTCATGATTGAACCCACTGAAAGTGAAAGCAAGgt----------ttaaataataaccttctctttatttctcgttctttttgtcagtttaaagtaaatggattg---tttgaacttctttttgcag--------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 12
lower sequence: EFJ19263 (Selaginella moellendorffii), 5'ss of exon 12
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag
 ||||||||||| || || |||||||| |||||||| ||||| ||||| ||||| || | ||| ||| | ||||| || ||||| || || || |||||||||   |  ||    |   |  || |  |||||    |   | ||| |  |   | | |                                           
CGTTGCAAAGCGTCTAATCGACTACGGCTTTCATGCGCCAACTATGTCTTGGCCAGTTCATGGGACATTGATGATCGAACCAACAGAAAGCGAGAGCAAGgtacagcaatatgtcatcctggttttgtttatg----catgtattcatcatgtttgtctcacag--------------------------------------

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|26058323|gb|CA801237.1|CA801237
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|120493515|gb|EH221682.1|EH221682
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|13480387|gb|BG509730.1|BG509730
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|22524910|gb|BU083721.1|BU083721
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|192315105|gb|FK009929.1|FK009929
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCAAAGCGCCTCATGGACTACGGTTTTCATGCACCAACAATGTCATGGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG