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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG

Basic information

species Glycine max
transcript GLYMA12G06980.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaattta----attaaaatgcatatacttttattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
  | | | |  | | |   | |  || |   |||| |   || | || | | |  |  || | |     ||||||||    |   |||| || | | |   ||||||||||  |||   || |  | |||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||  |||||||||| |||
--cttaagac-actaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcattt-cagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 1
aacatgacatgaatg-atgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaatta--aaatgcatatacttttattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
| |||    | ||||  |    | |  ||  |  |   |   | || ||   |  | | | | || |  |   | || | || ||||   |||   |    ||||||||  ||||   |  |  | || ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||  |||||||||| |||
atcatatagtcaatgtgtttcctgagttgtctgttgaatgaattttctttcttctgctcttaattgaccatttactgtaaattctttctatttgttt---tagATGTCATCGAGCCGCTTCTTGTAGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 3
-aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttattttccctgaac-agATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
 |   | ||| ||    |  | |||  ||  |  |||||   |  | |  |   | |  | | |||   |       | ||  ||  || |   ||    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||  |||||||||| |||
cagtctaaca-gatcactcttctcagttgtttc-tttttaaataatatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 10
aacatgacatgaatgatgctatcatgtgcatagtt----tttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
    ||  |  | |  || |    | |    | |         |  | |||||| |     || |   | | |   || | || ||||   |||   |    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||  ||||| |||| |||
-ttttggtacaagtattgttgatttctttggaatcagaaccaattaggttttagttcatgagttaggcactgattctgtaaattctttctatttgttt---tagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATATTCTACAAGCACAACTCTGTTAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 5
aacatgacatgaatgatgctatcatgtgcatagtt----tttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
    ||  |  | |  || |    | |    | |         |  | |||||| |     || |   | | |   || | || ||||   |||   |    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||  ||||| |||| |||
-ttttggtacaagtattgttgatttctttggaatcagaaccaattaggttttagttcatgagttaggcactgattctgtaaattctttctgtttgttt---tagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 3
aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttattttc--cctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
                |  ||  || | | || ||  ||    ||  |  || |    |||   ||  ||       |||||  |  ||      |   ||||||| || || |   | ||  | ||||||||||||||||| ||| | ||||| || ||||||||||||||||||||||||||||| || |||
---------------gta-tagtatcttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcagATGTGACTGAACCTCTTTTCGTCGAGGTTGATCAAATCTACCATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
--aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttatttt--ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
  |   |  |  || |     | |  |||  |  || ||  |||   | |  |   | |  |   | ||    ||   |||  |   ||||   |  | ||||||||| || ||||  |||||||| ||||||||||  || || |||||||| || || || ||||| || |||||||||||||||||||| |||
gtatggtctcgagactctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatcca---tcatcgtgatctctat-ttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 4
aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttattttcc-ctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG--------
   |||   |  |  || || |    ||  |  |  |  || |  |  |       |||  |||  |  |      |||| |||  ||||    | |||||||||||| |||| | | ||||| ||||||||||| || || ||||||||||| || |||||||| || |||||||| ||||||||||| |||        
-gtatggttttga-aattctctggcttgt-tgctgctattgagaatggaatattcctgtcttttgttctatccatttatattttggttttgggtttaacagATGTCACGGAGCCACTTTTGATCGAGGTTGATCAGATTTACCATCTTGCATGTCCTGCTTCTCCTATCTTCTACAAGTACAACCCTGTGAAGACAATCAA

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 4
-aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttt---tattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
  |  | | || |   |||  | ||  ||  || | |||   || |  |  |   |||  | ||  | | |   || | || |     | ||||| ||  ||||||||||| |||| ||||||||||||||||||| | || || || |||||||| || |||||||| ||||| || ||| |||| |||||||||
tcagttaagatca-caatga-accacttgt-taatcttttaatgataattcaca-gtttcatttctaatgattagcttttattccatattttttctcttcacagATGTCACTGAGCCATTGTTGATTGAGGTTGATAAGATATACCACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG

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|208312127|gb|GE107347.1|GE107347
EST:     C-ACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG                         ATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT
genomic: CAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATGgtataatttt ... ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT
EST: gi|213606684|gb|DB959073.1|DB959073
EST:     CAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG                         ATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT
genomic: CAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATGgtataatttt ... ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagatgcgttgtaatttaattaaaatgcatatacttttattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG
               atttaat  putative branch site (score: 4)
                                 tacttttattttccct  putative PPT
          ttgtaatttaattaaa  TA-rich tract