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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattgttaagctttatcatggtattaccacttcatatgatgttggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA

Basic information

species Glycine max
transcript GLYMA20G25120.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 17
---------------------------------------------------------tgtattgttaagctttatcatggtattaccacttcat-atgatgttggtaggcttatgtttgtatgcttctgattttatgttgtta-tgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
                                                           ||  |     ||||      | | | |  ||  |  || |      | |    || |  ||      ||  | | ||  ||  | ||   |  | | ||| ||||||| || |    ||| || || || || || || || ||  |  | |||||||||||||||||||| ||||||||||| ||| | ||  |||| |
gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggtttagtggttacagagtccctttggttctgcacttctgctcaaagattagacacattgagcaatataagttcatcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA

upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 17
tgtattgttaagctttatcatggtattaccacttcatatgatgttggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
                     |  |     | |||  |  ||  | ||   ||  |      ||  | ||| |||  || | || |    | ||   ||| | || || || |  |||||||| ||||| || || |||||||| ||| | |||||||||||||||||||| || || ||||| ||||||||  | || |
---------------------gtaagctgtatttcgca-aatacttgttttctactaacaacatattactg-tttcttgatattttttcctggt--ctagGTACCGTTCTCTAGAGTTGTATACATTGACCAATCTGACTTCCGAATGAAGGATTCAAAAGATTATTATGGGCTCGCCCCTGGTAAATCTGTTTTGCTAA

upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 18
---tgtattgttaagctttatcatggtattacc--acttcatatgatgttggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
   |  | | || | |  |||  || | | | |  |  ||| ||  || || |||  ||   ||| |  |    |||||||   || || | |  ||    |||| |||||||||| ||| |||| || ||||| ||  | || || |||||| ||||||| |||||||| ||||| ||||||||||| ||||||||  | ||||
ttttccaattttgatcactatactgttctgatcctatatcaaatattgctgttagtgttggatttctgag----tgattttgcatttttctcccctt-cctttagGTTCCATTTTCTAATATTGTGTACATTGAGCACACTGATTTTCGGATGAAAGATTCGAAAGATTACTATGGGCTTGCTCCTGGTAAATCTGTCCTGCTCA

upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 18
---tgtattgttaagctttatcatggtattaccacttcatatgatgttggtaggcttatgt-ttgtatgcttctgat--tttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
      | |         || |||    | || |  | |    || ||   || |||   | || ||  ||    ||  ||| | || |  ||  ||  || |||| | || ||||||||  ||||||| ||||| || || || || |||||| | ||||||||||| || ||||| ||||||||||| ||||| ||  ||||||
tggcaaagtagaggaacctaccat----taactatgtaactccatattca-agacttggatgttttaaactgtcaataatttttcttttgctgttttcatt-ttagGTGCCCTTTTCCAAAATTGTATACATTGAGCAGTCTGATTTTCGGATGAAGGATTCAAAAGACTACTATGGGCTTGCTCCTGGAAAATCCGTCCTACTCA

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|33389687|gb|CA852894.1|CA852894
EST:     CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG                         ATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
genomic: CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAGgtgaaattga ... ttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
EST: gi|14999379|gb|BI320344.1|BI320344
EST:     CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG                         ATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
genomic: CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAGgtgaaattga ... ttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
EST: gi|5753691|gb|AI960978.1|AI960978
EST:     CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG                         ATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
genomic: CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAGgtgaaattga ... ttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
                     ttctgat  putative branch site (score: 3)
                                            tttgttctt  putative PPT
                          attttatgttgttat  TA-rich tract