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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcagcttaattcaggtttttctttgaaaaattgccccttccacacttattccacatattgatatttttaatttttaacttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGA

Basic information

species Glycine max
transcript GLYMA04G01240.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 8
gtctgcagcttaattcaggtttttctttgaaaa--attgccccttccacacttattccacatattgatatttttaatttttaacttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGA
          |||| |   ||| ||||  ||     |||   || | ||| | | |       |||||   |||  |||||   |||||||||||||||| ||| | |||||  | |||||||||||||||||||| || || || |||||||| || || || ||||| ||||| |||||  | ||| | |
---------gtaatgccactttatcttctaattctgttgtttctcctacaatgagt-------ttgattacttt--ttttttttttttgcagTTTTATGTGGCAGAAGGGGAACTCTCATGTCAAATGTATCAGCGTTCAGCAGATATGGGCCTTGGTGTGCCGTTTAACATTGCTTCTTACTCTCTTCTTA

upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
gtctgcagcttaattcaggtttttctttgaaaaattgccccttccacacttattccacatattgatatttttaatttttaacttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGA
         ||| |       |  |||    | |||   ||||   || ||||  |    ||| | ||||||  |||||   | |||||||| ||||||   || |||||||||||||| |||||||| |||||||||||||||||||| || || || || ||||| |||||||||||||| || || |
--------gttagtattaaagtggcttatttatatt--tcctttatcatttatgtctttgatt-acatttttcctttttc-ttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA

upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 7
gtctgcagcttaattcaggtttttctttgaaaaattgccccttccacacttattccacatattgatattttta---atttttaacttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGA
|| || | | |   | |   | ||  |       || | | ||  ||  |  |   |   | || |  || |     | |||     |||||||||||||||||  | |||||| |||| ||||||||||||||||| |||||||| ||||| || || || |||||||| ||||| ||||||||  | ||||
gtttggaacatg-ctaattctctttatcatttttttcctcattttacggtagtaaaatgcaatgtttcttatttgcgtatttctacattgcagTTTTATGTAGCCAATGGGGAGCTATCCTGTCAAATGTATCAGCGCTCTGCTGATATGGGTCTTGGTGTGCCATTTAACATTGCTTCTTATGCTTTATTGA

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|20498259|gb|BQ273189.1|BQ273189
EST:     CATCTGATCTTAAATTAATGGCACTTCCACCCTGCCACATGTTTGCACAG                         TTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCT
genomic: CATCTGATCTTAAATTAATGGCACTTCCACCCTGCCACATGTTTGCACAGgtctgcagct ... acttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccccttccacacttattccacatattgatatttttaatttttaacttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGA
                                        ttttaac  putative branch site (score: 2)
                                              cttttgc  CT-rich tract
              ttattccacatattga  TA-rich tract