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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

Basic information

species Glycine max
transcript GLYMA06G17940.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 22
gttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccat-tttgcttc----agTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
              |||   |||||     | |      |  ||| | |||   ||| || | | |    ||| |  || | || |||    |||||||||| |||||||| ||||| || |||||||| ||||| || ||||| |||||||||||||| || || ||||| || || 
------------gtactccctttatagagctatgcagagttccagattgtt-cacatcttgaatactccttttgctgatatctgattctgacagTGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
gttagatatgcttcactgggtttattttaat-gtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA----------------
        |  || |||   |   |  || | |||  || | |   ||     ||      | ||| |   || |      || |  |||||||||||||| || || || |  ||||||||||| ||||| |||||||| ||||||||||| || || || || || || ||                 
-------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
gttagatatgcttcactgggtttattttaat-gtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
        |  || |||   |   |  || | |||  || | |   ||     ||      | ||| |   || |      || |  |||||||||||||| || || || |  ||||||||||| ||||| |||||||| ||||||||||| || || || || || || || 
-------gtattttactaaatgattgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
gttagatatgcttcactgggtttattttaatgtc-tctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
||  |||    | ||     |||   ||||||   | |    |    ||  || |  |   | ||  || || ||    | |   ||||||||||||| || || || ||||| || ||||||||||| ||  | ||||||||||| ||||| ||||| |||||  |||| || 
gtatgatggcatcca--aattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttt-tctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
gttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgctt--cagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
      ||    ||| | ||   |       | ||||||| |  |  |||||   || |  | |  |   | |    |   |  ||  |||||| ||||||| || ||||||| |||||||||||||||||| |||||||||||||||||||| || || || ||||| ||||| 
-----gtacttatcaattggacaa-------gcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 22
gttagatatgcttcactgggtttattttaat-gtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
  ||  | |||  |  |    | ||     | ||  | | | |    || || ||  |||   |||  |||    |      |    ||||||||||| ||||| |||||||| ||||||||||||||||| || ||||| |||||| ||||||| || || || || || || 
-gtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattacttt--gctgatttcaaccctgtaactataacagTGGTTTGGAGAGGGAGAAAAATATGTGAAAGCTGTTTTTTCACTTGCAAGCAAAATTTCTCCTAGTGTTATTTTCGTGGATGAG

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 21
---gttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
     |  |||  ||       |||  |    ||       |||       | | ||  ||| ||     |  | |||  | |   || |||||||||||||||||||| || || || |||||||| |||||  |||| ||||||||  | |||||||| || ||||| ||||| 
gtaactgaatactctatgaaaagttc-taccgat-------ttacacacgggatctttttttcaaacttgtgttcttcttaat--actgcagTGGTTTGGTGAGGGTGAGAAGTATGTCAAAGCTGTCTTTTCTTTGGCCAGTAAAATGTCCCCTAGCGTTATCTTTGTGGACGAG

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|15338257|gb|BI498913.1|BI498913
EST:     GCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAG                         TGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGT
genomic: GCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttagatatg ... tttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGT
EST: gi|27427279|gb|CA938799.1|CA938799
EST:     GTCAAGTATCACATCTAAG                         TGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGT
genomic: GTCAAGTATCACATCTAAGgttagatatg ... tttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGT
EST: gi|192318122|gb|FK010946.1|FK010946
EST:     AAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAG                         TGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGT
genomic: AAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttagatatg ... tttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA
                      ttttaac  putative branch site (score: 2)
                               cattcttttcccattt  putative PPT
                  ttcattttaa  TA-rich tract