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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

Basic information

species Glycine max
transcript GLYMA08G40380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                 |  |   | ||   | ||| ||  ||||       |||   | |||| |||  || |  |  || ||    | | | || | ||   |  | |  || | |  || ||||||||||||| || ||||| ||||||||||| || ||||| ||||| || ||||| ||||||||  | |||||||| || ||||| ||||||
--------------tggttgtgcctgctagcagtttgtagcaattcacc---cttaatgaaatgtttcagttttagtaagtgatg--gttactaatgtttc---cccactctttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatat-tataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                ||||| |      |||  ||     | |     ||     ||| ||  |   |  |  |||  |  ||   | ||| |  ||||| |||| |     | ||||  |||||||||| |||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||  | ||||| ||| | ||  | ||||||
---------------gctcatattgttcgatagattc----agtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaact--tttctatatcctctcggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattt---tgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                       | |    |  |   |   |||      ||  |    | || ||| ||| ||| |||  |     | ||| | |      | | |||   | |   | || || | ||||| ||||| || |||||||||||||||||||| ||||| ||||| || ||||| ||||| ||  | ||||||||||| ||||| || |||
---------------------aggcaagccttctccctgcaaatgcggagaggctc---gcataattatttcatt-tctagtgctgaagaatggttactaaaaccctaaggttctatatatctagGTCCTTGAGATGGATACCTACAGATACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                          |||| | |     ||  ||    | | ||||  || |      ||| ||||     ||  |       |    |||||     |||| ||   ||||| ||||| |||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||| | ||||||||  ||||  | || |||
--------------------aggacccttaaactagacgaggcttgacatcggttttgtgattccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtt--tcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                 | ||  ||  | |  | ||     | ||| |||     ||   ||| |||   || |  | || |  || ||  || | |   |  || |  |   | | || || | ||||| ||||| || ||||| |||||||||||||| ||||| ||||| || ||||| ||||| ||  | ||||||||||| ||||| || |||
----------------gtgataagtgataacttgttc----actttgtttgttggttcataattatttaatt-tcatgtgctgaataatggtt-actaaaccctcatgttctatgtatctagGTCCTTGAGATGGATACCTACAGGTACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
               | | | ||  | | | ||    |    |||| |     |||||    | || | ||   |  ||  |  ||||| |   |  |  | ||    ||||||| |  ||||| ||||| |||||||| ||||||||||| || ||||| |||||||| || || ||||| |||||||| |||||||| || ||||| |||||||||
--------------ttgtgaatt-caatcacatagcgttgacatttatcgtattttta----taatccattctctacctagtg-attatgaccaacata-ccattgccattattt-gcgcagATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
             | | | | | |||  | |  |||  ||       ||||  ||   |   | |||||||  |    | |   |||| |       |   ||  |   || || | | ||||||||||| |||||||||||||| ||||| || |||||||||||||||||||| |||||||||||||| || |||||||| ||||||||||| |||
-------------catataagtagtagctttggtttccaa-------tttattttcctgtgtttattctttcctatcatat-ggattacaga-agcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatatta--taattgatttctctatctt---aattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                      | || |  | ||  | |  ||||| | |  ||||| | | ||      | ||| | ||| | |||   |||||| ||| | | ||||   |||  |  ||| |||||||||||||||||||| || || |||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
---------------------ctttaatgttgttgct-agtaatttctct--cttttggcattg---tcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattctt-ttattctctgttatatta--taattgatttctctatctt---aattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                | |   || |     ||| ||| |     || || ||||    | |||  | |  | ||| |   | | |||   |||||||||| ||| ||||   |||  || ||| |||||||||||||||||||| || || |||||||| |||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||||
----------------cccgcctgca-----attctttca-----ttctttgctt--gagcatgtctgtcatcattttacatgagattgactaattgatttatctttcttctaaatgcttgtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGTACATACCGTACGCGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S201_84V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------gtaagtaaattaacctctcat-----ttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtcc-------agATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                                 |   ||  ||| | |||  |     | |   |||     |||      | ||  ||||||  |      || | |  |   |       || |  |||  |||| | ||| |||||| || ||        || || | || ||||| || |||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||||||||| ||||||||  |||||
gtaagtgatgctgttgttttcctaaccagcacatggatactttaccttcttctaatcatggggtttactccatttgctgtgtgttgcagctttacgt--cagttatgtcgtaaccgagatgcttttgcttgggttctttttctgaattatattttctggcatggagGTTTTGGAGATGGATACGTACAGATATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTACCGAACCCGTGATGAGATCTCTGGTGTACGACAG

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S47_1V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------gtaagtaaattaacctctca---tttgtact-tatattttttaagaatttttttagctttta-----ggaatgattcttttattctctgttat--attataattgatttctctatcttaa--ttatttt---gtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                         ||||  ||   | ||   |      || |  | |  ||  | || ||| |||  |  ||||     |   | ||| | || || |  |  ||  | | |  ||   || | | |  | |  ||||||     |  || |  | || ||||||||||| || || ||||| || |||||||| || || |||||||| ||||| || ||||| ||||| ||||||||  | || 
gtgtgtttacacgacgctcaacttctaagagaacacatctgaaagagcccgttcaatttgcttccttaggattgtttccgtatttactcacgttgtaattttgttgttgtgagcaatctactttgttttccttttttgttctgaacttatttctggatgaagGTCTTGGAGATGGACACATATAGGTATCATGGACATTCCATGTCCGACCCAGGCAGCACTTACCGAACTCGTGACGAGATCTCTGGTGTTCGTCAA

upper sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36226 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtc-cagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                                                                  |  | || | | | |    ||    || | | |||       ||      ||  ||| |  | |||||||| || ||  | || ||||| ||||||||||||||||| || || ||||| || ||| | || |||||||| || |||||||||
------------------------------------------------------------gtaagcttatctagtttttatatcttttggctttactcctcacgggggatgggaacgttacagGTGTTGGAAATGGATACTTATCGTTATCATGGGCACTCCATGTCTGATCCCGGGAGTACATATCGGACAAGGGAAGAGATTTCCGGCGTGAGACAG

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|4314061|gb|AI461180.1|AI461180
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATT                         ATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|6725662|gb|AW310061.1|AW310061
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATT                         ATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|10848193|gb|BF070736.1|BF070736
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATT                         ATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|7591537|gb|AW707268.1|AW707268
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATT                         ATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|7692225|gb|AW760338.1|AW760338
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATT                         ATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|5607004|gb|AI901102.1|AI901102
EST:     AAGGAGTTTGCTCTGAAGAATGGTCCCATT                         ATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AAGGAGTTTGCTTTGAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                                    tcttaat  putative branch site (score: 3)
                                             ttttgtcc  putative PPT
           tgttatattataattg  TA-rich tract