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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaagtctttattcatgtttggtggttttaattgtctcttgctattaaattaatatgaacattataacttacaagtgcacattagattgttaacttcaaaatccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCCATG

Basic information

species Glycine max
transcript GLYMA16G26920.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 6
gtatgtgaagtctttattcatgtttggtggttttaattgtctcttgctattaaattaatatgaacattataacttacaagtgcacattagattgttaacttcaaaatccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCCATG
          |  || |   | | |  |  | |  | | |   | |  | |  || | | |  |  |  | || |    ||   | ||   || || |  |        ||| ||||||||| |||||||||||||||||||| |||||||||||| |  | || ||||| || |||||  ||||||| || 
---------attattgtatgtatgttatattctccaatat---tggggactgtatgagtgtataggtgttgacctctttgttagcctttacttattgatgtt-------ctgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTAAGAAGGTTCTGCCGTACTACTGGGGCTGTTGCAATT

upper sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------gtatgtgaagtctttattcatgtttggtggttttaat-tgtctcttgctattaaattaatatgaacattataacttacaagtgcacattagattg---ttaacttcaaaatccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCCATG
                                                                        |   ||||   ||  || |   | |   |  ||| | | | | ||    ||     || || ||   |   |    ||    |   || ||| |   |||  | |  |     || ||||||||| |||||||||||||||||||| |||||||||||  |  |||| ||||| || |||||  ||||||| || 
gtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT

upper sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgtgaagtctttattcatgtttggtggttttaattgtctcttgctattaaattaatatgaacattataacttacaagtgcacattagattgttaacttcaaaatccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCC-ATG
                         |   || |  |   | || || |||  | |     |    ||| | | |     ||   ||||       | |   |  | |   |  | ||||| | |||||  |||||||||||||||||||||||||  | || |||||||| ||| | ||  |||| ||| || 
-------------------------gtatgtgtagaccatatcatgttat--actcgtcttagctattgttatt-----gtctgcatt------ctgataccccattttttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCGTACAGCGGGGGCTGTCGCCCAT-

upper sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
gtatgtgaagtctttattcatgtttggtggttttaattgtctcttgctattaaattaatatgaacattataacttacaagtg-cacattagattgttaacttcaaaa------tccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCCATG
                       |||    ||||  |  ||    | |    |   || | ||||| | ||   | || |||  |        | | ||||  |  |      | | ||||||||| ||||||||| ||||||||||||||||||||||||| || ||||||||||| ||||||||  |||||||  | 
-----------------------ttgcatcttttcttcatcaagggatgcatatccaagaagaacaatcta---tgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT

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|213599562|gb|DB962765.1|DB962765
EST:     AGTGGAGGAGCAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAA                         GCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG
genomic: AGTGGAGGAGCAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAAgtatgtgaag ... ctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG
EST: gi|193612736|gb|FK561353.1|FK561353
EST:     AGTGGAGGAGCAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAA                         GCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG
genomic: AGTGGAGGAGCAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAAgtatgtgaag ... ctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG
EST: gi|193323997|gb|FK291745.1|FK291745
EST:     CAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAA                         GCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG
genomic: CAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAAgtatgtgaag ... ctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG
EST: gi|26268510|gb|CA819573.1|CA819573
EST:     AGTGGAGGAGCAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAA                         GCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG
genomic: AGTGGAGGAGCAGTAGGAGAGATGGCGTTGCATTTCTGTGAGCGTTACAAgtatgtgaag ... ctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattataacttacaagtgcacattagattgttaacttcaaaatccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCCATG
                            tgttaac  putative branch site (score: 2)
                                          tccctgctt  putative PPT
                     attagatt  TA-rich tract