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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgctggctcattgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC

Basic information

species Glycine max
transcript GLYMA06G01120.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 4
atatgctggct--cattgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtgaacattttaaga-attgcttgatgc--ttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
 |    ||  |  |||  |    ||    | | |   |||| |   | ||| | ||  ||    |||||  | ||   || | | | || | || ||    |||||| ||||| || || || || ||||||||||||||||| ||||| ||||| || |||||||| ||| | || ||||| ||||| |||||||||||||| |
-tgcaatgaatgccataatgcccttgcaaattgtaatcttg-tgcatatattttactcaaa---tctgcatgagactgttctgacatatggattaatatcattagGTGGCAGAACCGTTGAGGGCTATGGTGATGGGAGCTCCTTTGGAAGATGCTCGCCATCTTGCCCAAAGATACGACAGGATGCGTCAGGAAGCCGAAGCAC

upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
atatgctggctcattgtcaatttatccagtttgtgcttgatt--tttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgc--ttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
   | |  | | | || ||   |||||  ||  | |||  |   ||||| ||| |||        | |  |  |    |||||||    ||    ||   | |||||||||| ||  | || || ||||| ||||||||||| ||||||||||| || || ||||||||| | || ||||||||||| || ||||| ||||| |
--ttacccg-taagtgccataatatcct-ttcatacttcgtacatttttttctaacaatcaaacccggacaaagcttgttttaagtgaagcgaactgacatcagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
atatgctggctcat-tgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgc--ttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
  ||  |  |   | || ||   |||||  | |    |||    ||||   | | || |    |   | |  |    ||||||| | | |    ||   | |||||||||| ||  | ||||| ||||| ||||||||||| |||||||||||||| || || || ||| | || ||||||||||| || ||||| ||||| |
--atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaa-gcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
atatgctggctcattgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtg-aacattttaagaattgcttgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
| || ||   | |  ||||||| ||    |  ||| |   ||  ||  |     ||   | ||  || | |  ||   | |   |||       |  ||||||||| ||||| ||| | ||||||||  ||||||||||||||||||||||  | |||||||||||||| |||||||||||||| || ||||| ||||| |
acatactctttaaaagtcaattaatgtcatg-gtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC

upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 4
---------atatgctggctcattgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
         || | |    ||||| | ||||  |||| ||  |  |   |||||     |   ||||||| |  |  |   |   ||| |     | ||| ||    |||||| ||| ||||||||||||||||| ||||||||||| ||||||||||| || |||||||||||||| ||||| ||||||||   |||||| ||||| |
ttaagacatatttacattatcattctaaattc-tccatttaatagtcagtttttcacctt--tataatgtgta-gttatccagtgtttga-----ttctttatttccagGTTGGAGAACCCTTAAGAGCAATGGTAATGGGAGCTCCCTTGGAGGATGCTCGACATCTTGCTCAACGATATGAGAGAATGCGAATGGAAGCTGAAGCTC

upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
-atat-gctggctcattgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
  |    ||   ||||| ||||||  | |  |     | |  ||  | |  | | | |  |  |  || |   ||     |   ||||  ||||||   |||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||||||||| ||||| |||||||| || ||||| ||||| |
cgtgccactttttcattttcaattattgc--tcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC

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|9987696|gb|BE661804.1|BE661804
EST:     CACAAATGGAGAAGGAGCGTGGGAACTTACTAAAAGCTCTTGGCACACAN                         GTTTGCAAAGCCCTTAA
genomic: CACAAATGGAGAAGGAGCGTGGGAGCTTACTAAAAGCTCTTGGCACACAGgtaaacacgc ... tgatgcttagGTT-GCAGAGCCCTTAA
EST: gi|18040044|gb|BM308338.1|BM308338
EST:     CACAAATGGAGAAGGAGCGTGGGAGCTTACTAAAAGCTCTTGGCACACAG                         GTTGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCC
genomic: CACAAATGGAGAAGGAGCGTGGGAGCTTACTAAAAGCTCTTGGCACACAGgtaaacacgc ... tgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC
                           aacattttaagaatt  TA-rich tract