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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattttgacctgaaacttttcttacatgttatatatgccagtatgacataccatatttgattccattgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

Basic information

species Glycine max
transcript GLYMA04G36360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
gtaagtattttgacctgaaacttttcttacatgttatatatgccagtatg---acataccatatttg-attccattgcattggttaaatgggtttatt--ccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
|| |||  | ||         |    || | |    ||  ||    | |       | |  || |||      ||||| |||  || ||  | |  |     |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgc-ttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
gtaagtattttgacctgaaacttttcttacatgttatatatgccagtatgacataccatatttgattccattgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
               |||   |  |  | |   | | |     | |||||   |||  |  |    |   ||| ||   | ||   ||| ||||  |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
--------------gtgagtttgctggttcggttaacacccttctgtatgctttacattcataagattgcttgtatatat-aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 4
gtaagtattttgacctgaaacttttcttacatgttatatatgccagtatgacataccatatttgattccattgcat-tggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
               |||   |  |  | || ||||      ||  |||| | | |     || ||   ||||| | |   |||   ||| ||||  |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
--------------gtgagtttgctggttca-gtta---gcacctatatg-cgtgcttacgttcataagattgcttgtatataagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtattttgacctgaaacttttcttacatgttat--atatgccagtatgacataccatattt---gattccatt--gcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
||||||| | |    |||   |||  | |    | |   || ||      | |   |   | ||    |||||  ||  |||  ||||||||   | |||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtatttt---gacctgaaacttttcttacatgttatatatgccagtatgacataccatatttgattccattgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
|| ||| |||    |   ||  |  |   | || ||  |    || || | | | |  |  |  |        |  || |||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||
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|15285557|gb|BI469448.1|BI469448
EST:     GAAATTGAGGTATTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
genomic: GAAATTGAGGTATTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCGgtaagtattt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
EST: gi|209720934|gb|BW682413.1|BW682413
EST:     GAAATTGAGGTATTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTA
genomic: GAAATTGAGGTATTGCAACAGCTTGGGAAACACGATAAAGGTAGCAATCGgtaagtattt ... ttccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacataccatatttgattccattgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT
            atttgat  putative branch site (score: 5)
                                         tttattcctt  putative PPT
          atatttgatt  TA-rich tract