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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttttacctgaaacttttcttgttatacatgccagtacgacataccatctttgattccagtgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

Basic information

species Glycine max
transcript GLYMA06G18530.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
gtaagtatt----tttacctgaaacttttcttgttatacatgccagtacgacataccatctttgattccagtgcattggtt----aaatgggtttatt--ccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
|| |||  |    || || |     ||| | |    ||  ||    | | |  |     ||||  || |     |||| ||    | ||  | |  |     |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgat-ctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
gtaagtatttttacctgaaacttttcttgttatacatgccagtacgacataccatctttgattccagtgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
    ||   ||| |  |      |||   | | ||    | ||| |   |||  || |    |    || ||   | ||   ||| ||||  |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
----gtgagtttgctgg------ttcggttaacacccttctgtatgctttacattcataagattgcttgtatatat-aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 4
gtaagtatttttacctgaaacttttcttgtt--atacatgccagtacgacataccatctttgattccagtgcat-tggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
                |  | ||| || |||   |     ||  || | | | |   | || ||   | ||| | |   |||   ||| ||||  |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
----------------gtgagtttgctggttcagttagcacctatatg-cgtgcttacgttcataagattgcttgtatataagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtatttttacctgaaacttttct--tgttatacatgcc------agtacgacata-ccatctttgattccagt--gcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
||||||| | |    |||   |||  |  ||    ||    |      |||    ||||    ||   |||||   |  |||  ||||||||   | |||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
-------gtaagtatttttacctgaaacttttcttgttatacatgccagtacgacataccatctttgattccagtgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
        | | || | ||        |||  | ||  |    || || |   | |  |  |  |           || |||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT

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|192330547|gb|FK021250.1|FK021250
EST:     GAAATTGAGGTACTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
genomic: GAAATTGAGGTACTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCGgtaagtattt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
EST: gi|15201058|gb|BI424670.1|BI424670
EST:     GAAATTGAGGTACTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
genomic: GAAATTGAGGTACTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCGgtaagtattt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgacataccatctttgattccagtgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
            ctttgat  putative branch site (score: 5)
                                         tttattcctt  putative PPT
                                ttaaat  TA-rich tract