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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcatttgtgacaaatccagaaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctagatagatgggtacatgtaggcatc...

Basic information

species Vitis vinifera
transcript Vv03s0038g04500.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 5'ss of exon 9
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcatttgtgacaaatccagaaacctaaccagttttgttcacatg-caaatttgctagaacgtttaaatatctagatagatgggtacatgtaggcatc----
|| ||||| ||||| || || |||||||| ||||| |||||||| || || ||||||||||| ||| | ||  | |||| |||||| ||||||||||| ||||||   || |     | || |  |  | ||  | |     || | | | ||  |  | ||    ||    | |  |  |||  | |   ||| |   |     
TCGTGCCAGATGTATCAACGCTCTGCTGATATGGGACTTGGTGTTCCATTCAACATTGCATCATATTCTCTTCTGACATACATGATTGCTCATGTTTGCGgtatg---ttatcttctaccctgctatgtgactggataatcccaaaggtctaaccttattgatgtattgttcagc--gtaagactgtttgttgttgatgttgtat

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 5'ss of exon 7
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatg----catttg-tgacaaatccagaaacctaaccagttttgttcacatgcaaattt----gctagaacgt-ttaaatatctagatagatgggtacatgtaggcatc
|||||||| |||||||| || |||||||| ||||| || |||||||| || ||||||||||| ||| | ||  | ||||| ||||| || || || |||||||||    || ||| | |    |  | |    | |   |||||    | |  ||||  |     |||||||   ||  | ||    ||   | |  |||          
TCATGCCAGATGTACCAACGCTCTGCTGATATGGGGCTCGGTGTGCCATTCAACATTGCATCATATTCTCTTCTGACATGTATGATTGCACAAGTGTGTGgtatgttctcacttgcttatctttttacaccggttattcgtttttcctaaagtcaaagcttcaaactagaacccattgcacatgctaattattcgtaaca----------

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA11G12280.1 (Glycine max), 5'ss of exon 8
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcat-ttgtgacaaatccag--aaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctagatagatgggtac-atgtaggcatc-----
||||| |||||||| ||||||||||| |||||||| || ||||| || ||||| |||||||||||||||||| | ||||||||||| ||||||||||||||||||||  || || ||  |   |  | || |||  | || | || | | ||| ||  || |      ||||||  |||  |  |||||| | ||  ||   ||     
TCATGTCAAATGTATCAGCGATCTGCCGACATGGGCCTGGGTGTCCCATTTAATATTGCATCTTATGCGCTCCTGACATGCATGATTGCTCATGTTTGTGgtatgcaaattatgccagctttcgctagacttaa--atttgtattgagacgcacat--gccat----cttaaat-cctactttcatgggttcgatagagttttctcatt

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA12G04480.1 (Glycine max), 5'ss of exon 9
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcat-ttgtgacaaatccag-aaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctaga--tagatgggtacatgtaggcatc--------------------------------------------------------------------------------------------
||||| |||||||| ||||||||||| |||||||| || ||||| || ||||| |||||||||||||| ||| | ||||||||||||||||||||||||||||||||  || || ||  |     | || |||  | || |  ||| | ||| ||    |   |  |   | | ||  |   |  || |  |  | |     |                                                                                             
TCATGTCAAATGTATCAGCGATCTGCCGACATGGGCCTGGGTGTCCCATTTAATATTGCATCTTATGCACTCCTGACATGCATGATCGCTCATGTTTGTGgtatgcaaattatgccagctttgctagacttaa--atttgtactcagacgcacataccatcttaaatccgactttcatgggttcaatagagatttctcattgtttgattgtagggaaatacagcttttatataaaaggaaaattgacattagatattggactgatcaatccatctgtcatatcctgtttttgtcag

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 9
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgca--tttgtgacaaatccag---aaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctagatagatgggtacatgtaggc-atc
||||| |||||||| |||||||||||||||||||| || || || || ||||| |||||||||||||| || || ||||||||||| ||||||||||||||||||||  ||  |||   ||       | || |||  | ||| ||  |  ||  ||  || |      |||     | ||  | ||  | || |||||  | || 
TCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaattattgaagcatttgctttagacttaaata-tttagtctat-tgataacatgttgtggt-tttgtgggtgtaattgga--gata-atgtatcccatt

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 9
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcatttgtgacaaatccagaaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctagatagatgggtacatgtaggcatc-----
||||| |||||||| |||||||||||||| ||||| || ||  | || ||||| |||||||||||||| || || ||||||||||| |||||||||||||||||||   |     || ||    |        | |||||  |    |  |  |    ||  |  || | | |||| ||| ||       | |||  |       
TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat----taagtcttttatttattatatttttggactttagttatgtgtggaggtcaattcagt-tctatatatattcccttttttagtaactgagaa

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ36491 (Selaginella moellendorffii), 5'ss of exon 8
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcatttgtgacaaatccagaaacctaaccagttttgttcacatgcaaat-ttgctagaacgtttaaatatctagatagatgggtacatgtaggcatc
|| ||||| ||||| || || |||  ||||||||| || ||||| || || |||||||| || || || |||||||| ||||||||||| || || |||||||||  || |  |||  | |      ||    | |  | ||    ||    | |||  | || |                                    
TCTTGCCAGATGTATCAACGCTCTTGTGACATGGGACTCGGTGTTCCATTCAACATTGCGTCCTACGCACTCTTAACTTGCATGATCGCGCACGTCTGTGgtatg--ttcgctacattttcttgtttctcgata-tgctatttggctgttcgtattgacaaaaag------------------------------------

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|33405951|gb|CF211578.1|CF211578
EST:     TAACATTGCATCTTATGCACTCTTAACATGCATGATCGCTCATGTTTGTG                         ACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
genomic: TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcattt ... tcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
EST: gi|352776732|gb|FQ472619.1|FQ472619
EST:     TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTG                         ACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
genomic: TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcattt ... tcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
EST: gi|33401638|gb|CF207265.1|CF207265
EST:     TAACATTGCATCTTATGCACTCTTAACATGCATGATCGCTCATGTTTGTG                         ACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
genomic: TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcattt ... tcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
EST: gi|110361466|gb|EC924940.1|EC924940
EST:     TAACATTGCATCTTATGCACTCTTAACATGCATGATCGCTCATGTTTGTG                         ACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
genomic: TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcattt ... tcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
EST: gi|110381698|gb|EC935151.1|EC935151
EST:     TAACATTGCATCTTATGCACTCTTAACATGCATGATCGCTCATGTTTGTG                         ACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
genomic: TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcattt ... tcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
EST: gi|33407075|gb|CF212702.1|CF212702
EST:     TAACATTGCATCTTATGCACTCTTAACATGCATGATCGCTCATGTTTGTG                         ACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
genomic: TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcattt ... tcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
EST: gi|110413975|gb|EC979795.1|EC979795
EST:     TAACATTGCATCTTATGCACTCTTAACATGCATGATCGCTCATGTTTGTG                         ACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC
genomic: TAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcattt ... tcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcatttgtgacaaatccagaaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctagatagatgggtacatgtaggcatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacctaa