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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagctccattgtcaacctatgacactttctgggccttcttcgttttttcattcaaatttacttagcatccttctcatcatttccatttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG

Basic information

species Glycine max
transcript GLYMA20G28200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 4
gtaagcagctccattgtcaacctatgacactttctgggccttcttcgttttttcattcaaatttacttagcatccttctcatcatttccat----ttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
                            | || ||||    | |  || || | |||    |||   |||| |  |||  ||| |||  ||    | |   |  |  |||  || ||||||||||||||||||||||||||  ||||   | || | ||||||||||||||| | |||||| ||||||| |   | 
-------------------gtaaggattagttcctgga---tatatgtgttattattggcttttg--tagctttgttcaaatcttttaaatgatatatgtatggaactttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 4
gtaagcagctccattgtcaacctatgacactttctgggcct-tcttcgttttttcattcaaatttacttagcatccttctcatcatttccatttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
               || |   |  |   ||   |     | || |  ||   |  |  |  |||  |||  ||| ||   || || |  ||         | | ||  || ||||||||||||||||||||||||||  ||||   |||| | || |||||||||||| | |||||  ||||||| |   | 
---------------gtaagaattggttcctggatatatatgtcattattgccttttgtagctttg-ttaaaatcttttaaatgatatatatga-------attgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 3
gtaagcagctccattgtcaacctatgacactttctgggcct-tcttcgttttttcattcaaatttacttagcatccttctcatcatttccatttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
   | ||| |     || |   |  |   ||   |     | || |  ||   |  |  |  |||  |||  ||| ||   || || |  ||         | | ||  || ||||||||||||||||||||||||||  ||||   |||| | || |||||||||||| | |||||  ||||||| |   | 
---aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttg-ttaaaatcttttaaatgatatatatga-------attgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcagctccattgtcaacctatgacactttctgggccttcttcgttttttcattcaaat---ttacttagcatccttctcatcatttccatttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
               || | |   | ||  || ||    ||   | || | | ||   || |   || |||        | |  | || |  | | |   ||   ||||| || |||||||||||||||||||||||||| ||||| ||  |  | ||  |||||||||||||| || || | |||||||  | |
---------------gtgagctcctaac--ttactcaatctatgt-gtatctgcaagaaagtactttccttgaagctagttttcttatgtg-actctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcagctccattgtcaacctatgacactttctgggccttcttcgttttttcattcaaatttacttagcatccttctcatcatttccatttttccttcac-tttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
                      || |   ||     |     ||| | | ||||||    ||| |   ||   |||| |  |||||| ||||  |     ||  ||| |||||||||||||||||||||||||||||||||||| || || |||||||| ||||||||||| || || |||||||| |  || 
---------------------gtaagttgctcatctgaataactttgctatttcatc---attga---agttcccttat--tcatttgcattcattgcctacactttcaagGTACAAATGGATGACATATGGAGAAGCAGGTACTGCTCGATCAGCAATTGGTTCTGGTTTAATATACTATGGAATACCGAAA

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|213598584|gb|DB964234.1|DB964234
EST:     GACTACAAATATCTGGGAACACGTGTCCGTGTTGATGGAACTGTTGGGGA                         GTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGG
genomic: GACTACAAATATCTGGGAACACGTGTCCGTGTTGATGGAACTGTTGGGGAgtaagcagct ... actttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaatttacttagcatccttctcatcatttccatttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
               catccttctcatcatt  CT-rich tract
     atttactta  TA-rich tract