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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtattgtattattgtgccaagtgtgtctgtccttgtaaagctgttgcacattcccttgtttgtttcagtacaatgttgattgtgattatgacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC

Basic information

species Glycine max
transcript GLYMA01G41620.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G41620.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
---agtattgtattattgtgccaa-gtgtgtctgtccttgtaaagctgttgcacattcccttgtttgtttcagtacaatgttgattgtgattatgacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC
      | ||||||    |||    || ||  |  | ||  || | | | || |  |        | ||       | | ||  || |||   ||    | |||||||||||| ||||||||||||| || ||| | |||||| | ||||| ||||| ||||| |||||||| ||||| |||||||   |||||||  ||||||
agccaaaatgtattcacatgctgctgtctgattcacttttgaatgttttggccctataatccaaatattgtgcataactatt--ttttgaccttgct--ttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC

upper sequence: GLYMA01G41620.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 2
agtattgtattattgtgccaagtgtgtctgtccttgtaaagctgttgcacattcccttgtttgtttcagtacaatgttgattgtgatt--atgacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC-----------------------------
                    | |||   ||||  ||||| ||| ||| ||           |  |||| ||  |  |||  | ||| |  ||     | ||||| |||||  |||||||||| ||||||||| | |||||| | ||||| || || || ||||||||||| ||||| ||||| |   |||||||  | ||||                             
-------------------gattgtacttgtcagtgtaatgct-ttgaac-----------tagttcactattaaattgtctctgactctatatttgttcagggttatgttgtttaccgtgtccgtgttagGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCCAGCTCAAGTTCCAGAGGAACAAGAGGTCT

upper sequence: GLYMA01G41620.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G034794_T01 (Zea mays), 3'ss of exon 2
-agtattgtattattgtgccaagtgtgtctgtccttgtaaagctgttgcacattcccttgtttgtttcagtacaatgttgattgtgat--tatgacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC
 |   ||  | | ||| |   | ||      |  |  |   |    || | || |  |    |  |||| ||  |  |||  | |||   |||     | ||||| |||||  |||||||||| ||||||||| | |||||| | ||||| || || || ||||||||||| ||||| ||||| |   |||||||  | ||||
gatagtttcagttttgagtagaatgaacagattgtactt--gtcagtgta-atgctttgaactagttcactattaaattgtctctgactctatatttgttcagGGTTATGTTGTTTACCGTGTCCGTGTTAGGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

upper sequence: GLYMA01G41620.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 2
agtattgtattattgtgccaagtgtgtctgtccttgtaaagctgttgcacattcccttgtttgtttcagtacaatgttgattgtgattatgaca-atg-cagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC
  || || |  | | ||  |    ||| ||   |  |  |    ||    ||    |      ||    |||||   |  ||| |||  |||   ||| ||||||| |||  | |||||||| ||||| ||  | ||||| || ||||| ||||| || || |||||||| ||||| ||||| |||||||||||||| || |
gttagtggagaaatatggaagcgttgtttga--tgattgaatcatttttaatctagtctcaaattctgttacaaatctagttgagatgttgatgtatgtcagGGCTTTGTTGTGTACCGTGTACGTGTGAGACGTGGTGGACGCAAGAGGCCAGTGCCTAAGGGTATTGTGTATGGTAAGCCAACAAACCAGGGAGTGACAC

upper sequence: GLYMA01G41620.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 2
agtattgtattattgtgccaagtgtgtctgtc--cttgtaaagctgttgcacatt--cccttgtttgtttcagtacaatgttgattgtgattatgacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC
  | || ||  ||| || |||    | |  |    |||  ||||      ||  |    ||| ||  ||| | || ||||   |     ||| |   | |  |||| ||||| || || ||||||||||||||  | ||||| || ||||| || |||||||| || ||||||||||| ||||| ||||||||||| || ||||
--tgtt-taaaattatgacaaactggcccattaatttgataagcatcaagacgatgattctttttactttgattataatgccaaacactattttc-tattttagGGGTATGTTATCTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTTCCCAAGGGCATTGTTTATGGAAAGCCTACAAACCAGGGTGTCACCC

upper sequence: GLYMA01G41620.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0551g00020.t01 (Vitis vinifera), 3'ss of exon 2
agtattgtattattgtgccaagtgtgtctgtccttgtaaagctgttgcacattcccttgtttgtt---tcagtacaatgttgattgtgattatgacaatg-cagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC
    |   || | | |  | |    ||    |    |  |     |   | |    ||| ||| |   ||   ||||     | | ||  | |     |  ||||| ||||||||||| ||||||||||||||  | ||||| || ||||| || || ||||| || ||||||||||| |||||||||||||| || |||||||
----tctaatcactctctcgatccagttctgctgcttgtaatctataagcctggaattggttgctatatctacacaaatgacactctggatgtactgttttcagGGTTATGTGATTTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTGCCCAAGGGAATTGTTTATGGTAAGCCCACAAACCAAGGTGTTACCC

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|8827482|gb|BE211212.1|BE211212
EST:     GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAG                         GGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
EST: gi|15287650|gb|BI471541.1|BI471541
EST:     GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAG                         GGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
EST: gi|12689256|gb|BG155592.1|BG155592
EST:     GGTCGACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAG                         GGCTATGTGATATACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGGCCA
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
EST: gi|23729345|gb|BU762755.1|BU762755
EST:     GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGTTAAGCAG                         GGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
EST: gi|7796785|gb|AW782179.1|AW782179
EST:     GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAG                         GGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
EST: gi|31561369|gb|CD487207.1|CD487207
EST:     GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAG                         GGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
EST: gi|207810578|gb|GD781687.1|GD781687
EST:     GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAG                         GGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGT
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGT
EST: gi|14258879|gb|BG881787.1|BG881787
EST:     GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAG                         GGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA
genomic: GGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatt ... gacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacattcccttgtttgtttcagtacaatgttgattgtgattatgacaatgcagGGCTATGTGATTTACCGTGTTCGTGTTAGGAGGGGTGGCCGAAAGAGACCAGTTCCCAAAGGTATTGTTTATGGGAAGCCCACAAACCAGGGAGTTACCC
                             tgttgat  putative branch site (score: 4)
              tttgttt  TA-rich tract