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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtattatctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC

Basic information

species Vitis vinifera
transcript Vv18s0001g02700.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------gtttgttcctgtcaatattgcatttc-atggttattttggagggcccatccagctta--agttttgtattat-ctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
                                    ||  ||  | |   | | | |  |  || |  || | | |  | |     |  | |  |   |  |  |||  | | ||| ||||||||| || |||||||||||| ||||||| || ||||||||||||||||| ||||| || || ||||||||||||||||| || |||||| ||||||||
gtatttacatacatatattttcacagccatgtggaattcttttttttttttttagaaaatggatagccatgtggaaatgtcttcagaaatcatcatgctgatgctatgttcatttcccagCTTGGTGAAGTTCTTGACACCTTCATCTGGGCTTCAAGGATACTGGGATCCATACCCGATCGACATGGAATTTCGACCACCATGCATGGTGTTGTCAACC

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 7
----gtttgttcctgtcaat--attgcatttcatggtt----attttggagggcccatccagcttaagttttgtattatctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
     |   | | | ||||   |   ||  |     ||    |||||  |     ||||  ||| | | | | | | ||||   || |||||||||| || |||||||||||||||||||| |||||||| ||||||||||| |||||||| || ||||| |||||||| || || |||||  ||||||||
gtatttacatacatatcaactaaggacaactggccattgaaaatttttcacaaatcatcatgctgatgctatat-tcatct---ttgtcagCTTGGTGAAGTTCTTGACACCTGCATCTGGGCTCCAAGGGTACTGGGATCCTTACCCCATCGACATGGAGTTTCGACCGCCATGCATGGTCTTGTCAACC

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G038487_T01 (Zea mays), 3'ss of exon 7
gtttgttcctgtcaatattgcatttcatggttattttggagg---gcccatccagcttaa---------gttttgtattatctgaattct--cagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
|| ||| ||| |  || |  | | | |    ||  |          | | ||||   ||          |  |  | |  | |   ||||  ||| ||||| || ||||| |||||||| ||||| |||||||| ||||||||||| ||||| || || ||||| || ||||| || ||||||||  |||| |||
gtatgtacctttgcatctcacttgtgaaaactaactgacgaatatacacttccataatatcaccatggtggctgatgtcgtgttgtttctgtcagTTTGGTGAAGTTCTTAACACCTGCGTCTGGGCTCCAAGGGTACTGGGATCCTTACCCGATCGACATGGAGTTCCGACCGCCATGTATGGTCTTGTCGACC

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
--------------gtttgttcc----tgtcaatattgcatttcatggttattttggagggcccatccagcttaagtt-ttgtatt-atctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
              ||||  |       || |||  |    || ||  |  |  |  |   |     ||| | |     ||| ||  || |||| |  ||||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| || || |||||||| |||||||||||||| ||||| || ||||||
gatggatgaacaaggtttaatttaaggcgtaaat-ctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
-----------------------gtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtatta-tctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
                        |  | || |  |  |||   ||   |   | | |||| ||  | ||  |||  |     ||| || | | |||| |  ||||||||| || || ||||||||||||||||| || |||||||||||||||||||| || || |||||||| |||||||||||||| ||||| || ||||||
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtag--ctcactcagtct---ccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G23860.1 (Glycine max), 3'ss of exon 7
----------------------gtttg-ttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtatta-tctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
                      ||| |  || |  |  |||   ||   |   | | |||  ||  | ||  |||  |     ||| || | | |||| |  ||||||||| || || ||||||||||||||||| || |||||||||||||||||||| || || |||||||| ||||||||||| || ||||| || ||||||
taatggaatagttcagccttttgttaggctcttaactttatcttataaaacaataaatttctag--ctcactcagtct---ccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATCGATATGGAGTTTCGACCACCCTGCATGGTACTATCAACC

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 7
-------------gtttgttcctgtcaatattgcatttcatggttattttggagg-gcccatccagcttaagt----tttgtatt-atctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
              ||  ||   | ||  | |  |     |   |  |    ||   |   ||  | | | ||    |  | ||  || |||| |  ||||||||| ||||| ||||||||||||||||| || |||||||||||||| ||||| || || |||||||| ||||| |||||||| ||||| || ||||||
tggataaaacgagattaatttaaggcataaatctaagctttatcttctgaaaagatacatttcttggtcacgtagtctcagcatggatttgaacttgcagCTTGGTGAAATTTTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGGCCACCTTGCATGGTTCTATCAACC

upper sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 7
gtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtattatctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
    ||| || | ||   |   |    || | | |    ||     |    | ||||| ||| | || |  | | |  ||| ||||| || || || |||||| | || || |||||||||||||||||||| || || || ||||||||||||  |||||| ||||| ||  | || || 
----gtttcttttaactctcattactctgttcagtgctaagatgaaacttggtttaagctttctgtttttggtactg-cagTTTGGTGAAGTTTTTAACACCTACCTCGGGTCTCCAAGGATACTGGGATCCATATCCAATCGATATGGAATTTAAACCACCGTGTATTGTTTTATCGACA

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|110712590|gb|EE090383.1|EE090383
EST:     GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAG                         CTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
genomic: GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcct ... gaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
EST: gi|351052221|gb|FQ452375.1|FQ452375
EST:     GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAG                         CTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
genomic: GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcct ... gaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
EST: gi|349827565|gb|FQ422433.1|FQ422433
EST:     GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAG                         CTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC
genomic: GCCCCTTTCACTCATACATCCACCTTTGCCAAAGGATGGAGCGTGCCTAGgtttgttcct ... gaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttattttggagggcccatccagcttaagttttgtattatctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC
                                                ttctc  CT-rich tract
                           ttaagttttgtattat  TA-rich tract