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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaatgcattgttgtccatgttttagctttttatatacttgctagattgttgatatttatttatttctgtaatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTACTTACCAGTCATTCATGCAAATGTGTATCAGACAATAAAA

Basic information

species Glycine max
transcript GLYMA17G34450.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34450.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g26890.1 (Oryza sativa), 3'ss of exon 1
--------------gtaagaaaatgca--ttgttgtccatgttttagctttttatatac-ttgctagattgt-tgatatttatttatttctgtaatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTACTTACCAGTCATTCATGCAAATGTGTATCAGACAATAAAA
                 ||   ||| |  || |  ||||||    | | |  |   |||   ||||| | || |||| | |  ||| |  |   |  ||||||| || ||  | || |||||||||||||| ||||||||||| |  ||||||  | |||| || |||||||| || ||||||||||| |||
gtctacgatatttaaacaggtgatgaatgttatattccatggagaatcataatccgtacgccgctagttagtctgatgtattcttactgttc--acctgcagATTAAGCTCCTTTTCCAAACTGGCTTTGATGAGGCAGAACTTAGGAGCTACACATCAGTTATCCATGCAAACGTCTATCAGACAATTAAA

upper sequence: GLYMA17G34450.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G064732_T04 (Zea mays), 3'ss of exon 4
gtaagaaa-atgcattgttgtccatgttttagctttttatatacttgcta-gattgt---tgatatttatttatttctg-taatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTACTTACCAGTCATTCATGCAAATGTGTATCAGACAATAAAA----------
|||||    ||||       |  | | |     || |||| |  |    | ||  |    | |    | | | || | | | ||  ||||||||| ||| | || ||||||||||||||||||||||| || |  ||||||  | ||||||| ||||| ||||||||||||||||| |||          
gtaaggtttatgccactccctagaggatcataattcttatgtcatcatcaagacagcaagtcacggatgtgtcttaccgctcattcgcagATAAAGCTTCTTTTCCAAACTGGCTTTGACGAGGCAGAGCTTAGGAGCTACACATCAGTCATCCATGCTAATGTGTATCAGACAATTAAAGTATGCTATA

upper sequence: GLYMA17G34450.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G064732_T01 (Zea mays), 3'ss of exon 4
gtaagaaa-atgcattgttgtccatgttttagctttttatat-acttgctagattgt---tgatatttatttatttctg-taatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTACTTACCAGTCATTCATGCAAATGTGTATCAGACAATAAAA
|||||    ||||       |  | | |     || |||| | |    | |||  |    | |    | | | || | | | ||  ||||||||| ||| | || ||||||||||||||||||||||| || |  ||||||  | ||||||| ||||| ||||||||||||||||| |||
gtaaggtttatgccactccctagaggatcataattcttatgtcatcatcaagacagcaagtcacggatgtgtcttaccgctcattcgcagATAAAGCTTCTTTTCCAAACTGGCTTTGACGAGGCAGAGCTTAGGAGCTACACATCAGTCATCCATGCTAATGTGTATCAGACAATTAAA

upper sequence: GLYMA17G34450.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G26300.1 (Arabidopsis thaliana), 3'ss of exon 4
---------gtaagaaaatgcattgttgtccatgttttagctt-tttatata-cttgctagattgttgatatttatttatttctgtaatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTACTTACCAGTCATTCATGCAAATGTGTATCAGACAATAAAA
           | ||||||  |||||  ||  |  || |  ||  ||||  | | |||||  |   |||||   ||||| |     ||| |||||||||||||| | || ||||| || ||||| || | ||||||||| |||||  | |||||||||||||| ||||| |||||||| ||||||
gcaagtccacaaggaaaattgattgtactctttacttaaatttacttatgaatcctgctaattgaatgatacaaatttact-----aatttgcagATAAAACTTCTATTCCAAACGGGATTTGATGAAGGAGAACTAAAGAGCTATGTTCCAGTCATTCATGCCAATGTCTATCAGACTATAAAA

upper sequence: GLYMA17G34450.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g02040.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtaagaaaatgcattgttgtccatgttttagctttttatatacttgct-agattgttgatatttatttatttctg--taatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTACTTACCAGTCATTCATGCAAATGTGTATCAGACAATAAAA
                |       ||| |||||    | ||   | | ||||| | |   | |  ||| || ||||| ||  || | | ||  |    ||||||||||||||||||||||||||||||||||||||||||| ||||| |||||  |  ||||| | ||||| ||||| |||||||||||||||
gcaagtcataatattagccgtcccatgaattgtgtagcttgcacttg-tttttctctgtatacagagaatgctgatacttcattttatgtgattggcgtgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAGCTAAAGAGCTATATCTCAGTCGTCCATGCCAATGTATATCAGACAATAAAA

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|207695990|gb|GD676911.1|GD676911
EST:     GAGCTGGAGAGTCAGGGAAGTCCACAATATTTAAGCAG                         ATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTAC
genomic: GAGCTGGAGAGTCAGGGAAGTCCACAATATTTAAGCAGgtaagaaaat ... taatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTAC
EST: gi|193522163|gb|FK479866.1|FK479866
EST:     GAGCTGGAGAGTCAGGGAAGTCCACAATATTTAAGCAG                         ATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTAC
genomic: GAGCTGGAGAGTCAGGGAAGTCCACAATATTTAAGCAGgtaagaaaat ... taatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTAC
EST: gi|207695379|gb|GD678120.1|GD678120
EST:     GAGCTGGAGAGTCAGGGAAGTCCACAATATTTAAGCAG                         ATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTAC
genomic: GAGCTGGAGAGTCAGGGAAGTCCACAATATTTAAGCAGgtaagaaaat ... taatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttttatatacttgctagattgttgatatttatttatttctgtaatatgcagATAAAACTTTTGTTTCAAACTGGCTTTGACGAGGCAGAACTAAAAAGCTACTTACCAGTCATTCATGCAAATGTGTATCAGACAATAAAA
                       tgttgat  putative branch site (score: 4)
                                       tttctgt  putative PPT
                     attgttgatatttatt  TA-rich tract