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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattggagggccagcttctgattaatttctttctttgatttcgttactgattagttttctgttatttgcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAG

Basic information

species Vitis vinifera
transcript Vv18s0001g08600.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g51910.1 (Oryza sativa), 3'ss of exon 4
gtaa-ttggagggccagcttctgattaatttctttctttgatttcgttactgattagttttctgttatttgcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAG
|||| ||            |   |  || |  |       || | ||  |||   |  || ||||| |   |  | | |||| ||||| |||||||| |||||||||||||| |||||||||||||||||||| ||||  || ||||||
gtaaatttcttcttttatctgcaagaaaatcttcgagactatcttgt-gctgtgcaacttactgttgtcccc--tcacagATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G092091_T02 (Zea mays), 3'ss of exon 2
gtaattggagggccagcttctgattaatttctttctttgatttcgttactgattagttttctgttatttgcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAG
|||| |           |  ||   |   | | ||    | | |  || |   ||  || |   | | |        |||| ||||| |||||||| ||||| |||||||||||||| |||||||||||| |||||| ||| || |||
gtaacttctcctttgtttggtg-cgagcatttctcaaaaactcctctagtccatacattacaagtttctttcg-ggcagATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G385543_T01 (Zea mays), 3'ss of exon 4
gtaattggagggccagcttctgattaatttctttctttgatttcgt-tactgattagttttctgttatttgcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAG
||||           | ||      |    ||| |       |||| || |    |  || |   | | |     || |||| ||||| |||||||| ||||| |||||||||||||| ||||| |||||| |||||| ||| || |||
gtaac-atctcctttgtttggtgcgagcaacttcccaaagactcgtgtaatccacacattacaaatttctttcg-aatagATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G05090.1 (Glycine max), 3'ss of exon 5
gtaattggagg-gccagcttctgat-taatttct-ttctttgat--ttcgttactgattagttttctgttatt-tgcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAG
|| ||| |||  |   |  | ||   |  ||||| ||| | |||  ||  |     |||| |||| ||||||  |    |   |||  || || || || |||||||| ||||||||||| || ||||| || |||||||||||||||||||||
gttatttgagatgattgtatttgtcatggtttctattcatagatgatttctggtatattaattttatgttatcattggctttcagAAAACGGGTAAAGCGGTAATGCTGGATGAGATTATAAACTATGTGCAATCACTGCAACAACAGGTTGAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G05180.1 (Glycine max), 3'ss of exon 4
----------gtaattg-gagggcca-gcttctgattaatttctttctttgatttcgttactgattagttttctgttatt-tgcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAG
           | |||| |   | || | ||   | |||| |  |  |  |||||| |     |||| |||| || | |  |    |   |||| || || || || |||||||| ||||||||||| || ||||| || | |||||||||||||||||||
gttatttgagatgattgtgtttgtcatgatttcaaataatgtagtgat--gatttc-tggtatattaattttatgctgtcattggctttcagATAACGGGTAAAGCGGTAATGCTGGATGAGATTATAAACTATGTGCAATTACTGCAACAACAGGTTGAG

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|161708702|gb|FC059231.1|FC059231
EST:     TCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG                         ATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCA
genomic: TCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAGgtaattggag ... gcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCA
EST: gi|349819168|gb|FQ412062.1|FQ412062
EST:     TCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG                         ATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCA
genomic: TCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAGgtaattggag ... gcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCA
EST: gi|351053379|gb|FQ455715.1|FQ455715
EST:     TCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG                         ATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCA
genomic: TCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAGgtaattggag ... gcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttctttctttgatttcgttactgattagttttctgttatttgcaataaaagATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAG
                      tactgat  putative branch site (score: 2)
                                       ttatttgcaataaaa  TA-rich tract