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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaatatctgttaactggtctagtttcttgtctcacttcaacttgtttggattctaatttgtatgtcttgggaaataacttatgttctctatccagGATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGACTCAGAGAAGGTCCAACAATTGTGTGATGCAGCCAATCAGGAAGTTCCTG

Basic information

species Glycine max
transcript GLYMA18G06500.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G06500.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 5
gtaagcaatatctgttaactggtctagtttcttgtctcacttcaacttgtttggattctaatttgtatgtcttgggaaataacttatgttctctatccagGATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGACTCAGAGAAGGTCCAACAATTGTGTGATGCAGCCAATCAGGAAGTTCCTG
     || | ||     |      |    | | ||||  ||| |  || ||||  ||| ||  ||  ||| |         | || | || ||| |  |||||||  | |||||||| || ||||||||||| |||||||| || || || ||||||||||| || ||||| || ||||| || ||  |||||||   ||
---gtcactgtccaaagaacaccgtgagatat-gtctaccttgagatt-tttgctttccaaactgattgttt---------atttttattatctgtgtagGATGCTTCAGATGCTGCCAGCAGTGCTATGGTCAGTGTGATTGGTCTAGATTCAGAGAAGGTGCAGCAATTATGCGATGCTGCTAACGAGGAAGTAGATG

upper sequence: GLYMA18G06500.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30200.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------gtaagcaatatctgttaactg-gtctagtttc--------ttgtctcacttcaacttgtttg-gattcta------atttgta----tgtcttgggaaataacttatgtt-------ctctatccagGATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGACTCAGAGAAGGTCCAACAATTGTGTGATGCAGCCAATCAGGAAGTTCCTG
                   |    |   |   || |||  ||| |||||         ||||  |   | |||||  | | |||  ||      ||| | |    ||  |||     ||  || || |       || | | |||| ||| || ||||||||||  ||||| ||||||||| | |||||  |||||||||| ||||| || || |||||||||||||| ||||| |||||   ||
gtaagattgaactctgctctgtatatccttcattgactatgtcaagtttaggttgatgttgtgacggctgaactttgtagtgatcttatataccattcgaacagctgcattgacttttagtttttgataaaatgactttcttcagGCTGCTGCAGATGCTGCTAAGAGTGCCATGGTTAGTATCATAGGGTTGGACTCAGAAAAGGTTCAGCAGTTGTGTGATGCAGCAAATCAAGAAGTAGATG

upper sequence: GLYMA18G06500.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g07380.t01 (Vitis vinifera), 3'ss of exon 5
gtaagcaatatctgttaactggtctagtttcttgtctcacttcaacttgtttggattctaatttgtatgtcttgggaaataacttatgttctctatccagGATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGACTCAGAGAAGGTCCAACAATTGTGTGATGCAGCCAATCAGGAAGTTCCTG
    | |  ||| ||||  |   ||| |   || ||| | ||           || ||   ||||||  | |     | |    | ||      ||| ||||||| || |||||||||| |||||||||||| ||||| || ||||| || ||||| || |||||||  |||||||||||||||||| | ||||||  ||
----gtaccatcagtta--ttacctaatgggttatcttaattttga--accaagaatccc-tttgtaactat-----atttctatgtggctgtcatc-agGATGCTGCCGATGCTGCTAAAAGTGCTATGGTCAGTGTCATTGGACTAGATTCAGAAAAAGTCCAACTGTTGTGTGATGCAGCCAATGAAGAAGTTGATG

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|19054193|gb|BM732860.1|BM732860
EST:     CTTTGAAGATGGACTCAAGTTGGTCAAACTGANGGGAGAGGGCATGCAN                         GATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGAC
genomic: CTTTGAAGATGGACTCAAGTTGGTCAAACTGAGGGGAGAGGCCATGCAGgtaagcaata ... ctctatccagGATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGAC
EST: gi|26048193|gb|CA784752.1|CA784752
EST:     CTTTGAAGATGGACTCAAGTTGGTCAAACTGAGGGGAGAGGCCATGCAG                         GATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGAC
genomic: CTTTGAAGATGGACTCAAGTTGGTCAAACTGAGGGGAGAGGCCATGCAGgtaagcaata ... ctctatccagGATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttggattctaatttgtatgtcttgggaaataacttatgttctctatccagGATGCCGCTGATGCTGCTAGAAGTGCTATGGTTAGTGTGATAGGACTGGACTCAGAGAAGGTCCAACAATTGTGTGATGCAGCCAATCAGGAAGTTCCTG
                               aaataac  putative branch site (score: 2)
                                           ttctctatcc  putative PPT
         attctaatttgtat  TA-rich tract