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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttccctttattgtccaagttcaatctattctacctgtaaaagttgcagagttttttatcagatattttatgcttgattattcttatggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTTGGTTTTAAAATCAGCAGCAAAAGCATTTCAG

Basic information

species Glycine max
transcript GLYMA10G41940.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41940.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os05g05200.1 (Oryza sativa), 3'ss of exon 14
gtatgtttccctttattgtccaagttcaatctattctacctgtaaaagttgcagagttttttatcagatattttat--gcttgatt--attcttatggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTTGGTTTTAAAATCAGCAGCAAAAGCATTTCAG
||| |||   || ||   |  |   |   | | ||      | || || |  ||  ||| | || |  ||   | |    ||||||  ||||| ||  ||   ||||||||| |||||||||||||||| || || ||||| ||| |||||||  |  |  | || ||   | | ||    || |||
gtaagtt---ctgtaaaatttataattgttatttttgtttggcaacagct--aggttttatgatgacttacgatgtcaatttgattgcattctcataaac---agGAAACTTATTTCATGGGCATGGTTAACATGCTTATTTTTCGTCCCTGAAATATTGGTCAAGTCTCTATCCAACAAGTTCCAG

upper sequence: GLYMA10G41940.2 (Glycine max), 3'ss of exon 14
lower sequence: AT1G57600.1 (Arabidopsis thaliana), 3'ss of exon 14
gtatgtttccctttattgtccaagttcaatctattctacctgtaaaagttgcagagttttttatcagatattttatgcttgattattcttatggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTTGGTTTTAAAATCAGCAGCAAAAGCATTTCAG
|||    ||||||   |  | | | |   | | |  |   || |  | | |  |    |||         |  |||| |||| |  | |  | |     ||||| |||||||||||||||||||| || |||||||||||||| || ||  || |  | ||||||||| | |  |||| | ||
gtaa---tcccttgccttcctatgattcctttgtgttgtatgaatcattcgatgcaactttc--------tcatatggttgactgctgtgtttgcaaccagGAAGCTTCTTTCATGGGCATGGTTAACATGTTTATTCTTCATGCCAGAAATGTTACTGAAATCAGCATCCAGTGCATATAAG

upper sequence: GLYMA10G41940.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv00s0581g00010.t01 (Vitis vinifera), 3'ss of exon 5
-----gtatgtttccctttattgtccaagttcaatctattct--acc-tgtaaaagttgca-gagttttttatcagatattttatgcttgat----tattcttatggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTTGGTTTTAAAATCAGCAGCAAAAGCATTTCAG
        || ||       || |||||  ||| | | | ||  ||  || |||||  | | || |||||||     ||||       |||     ||||  | | ||||||||||| |||||||||||||||||||| ||||||||||||||  | || ||| || |  | ||||||   |||||  ||||||||
gtactacttgctttttcaagttttccaatgtcactttttccttgacagtgaaaaagaagtatgaattttttaaatcctattcctcatctgacagtgtattggttttgaccttagGAAGCTTCTTTCATGGGCATGGTTAACGTGTTTATTCTTTGTTCCAGAGATGATACTGAAATCATTGGCAAATACATTTCAG

upper sequence: GLYMA10G41940.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv00s0449g00010.t01 (Vitis vinifera), 3'ss of exon 8
-----gtatgtttccctttattgtccaagttcaatctattct--acc-tgtaaaagttgca-gagttttttatcagatattttatgcttgat----tattcttatggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTTGGTTTTAAAATCAGCAGCAAAAGCATTTCAG
        || ||       || |||||  ||| | | | ||  ||  || |||||  | | || |||||||     ||||       |||     ||||  | | ||||||||||| |||||||||||||||||||| ||||||||||||||  | || ||| || |  | ||||||   ||||| |||||||||
gtactacttgctttttcaagttttccaatgtcactttttccttgacagtgaaaaagaagtatgaattttttaaatcctattcctcatctgacagtgtattggttttgaccttagGAAGCTTCTTTCATGGGCATGGTTAACGTGTTTATTCTTTGTTCCAGAGATGATACTGAAATCATTGGCAAATGCATTTCAG

upper sequence: GLYMA10G41940.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv00s0507g00020.t01 (Vitis vinifera), 3'ss of exon 8
-----gtatgtttccctttattgtccaagttcaatctattctacc-tgtaaaagttgca-gagttttttatcagatattttatgcttgat----tattcttatggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTTGGTTTTAAAATCAGCAGCAAAAGCATTTCAG
        || ||       || |||||   |  | |  |  ||  || ||| |  | | ||  ||||||     || |       |||     ||||  | | ||||||||||| |||||||||||||||||||| ||||||||||||||  | || ||| || |  | ||||||   ||||| |||||||||
gtactacttgctttttcaagttttccaatcactttttccttgacagtgaaaacgaagtatgaaatttttaaatcctactcctcatctgacagtgtattggttttgaccttagGAAGCTTCTTTCATGGGCATGGTTAACGTGTTTATTCTTTGTTCCAGAGATGATACTGAAATCATTGGCAAATGCATTTCAG

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|58019147|gb|CX705889.1|CX705889
EST:     AATGTGTGGGTTGTTTTCACATTTGTTGCAATCTGGCATGATTTAGAGTG                         GAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTT
genomic: AATGTGTGGGTTGTTTTCACATTTGTTGCAATCTGGCATGATTTAGAGTGgtatgtttcc ... tggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTT
EST: gi|58018861|gb|CX705603.1|CX705603
EST:     AATGTGTGGGTTGTTTTCACATTTGTTGCAATCTGGCATGATTTAGAGTG                         GAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTT
genomic: AATGTGTGGGTTGTTTTCACATTTGTTGCAATCTGGCATGATTTAGAGTGgtatgtttcc ... tggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgcagagttttttatcagatattttatgcttgattattcttatggaccttagGAAACTTCTTTCATGGGCATGGTTGACGTGTTTATTCTTCATCCCTGAGTTGGTTTTAAAATCAGCAGCAAAAGCATTTCAG
                              gcttgat  putative branch site (score: 5)
                                       ttcttat  putative PPT
        agttttttatcagata  TA-rich tract