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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgtatatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaagtgattgagctg...

Basic information

species Vitis vinifera
transcript Vv15s0046g02410.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os02g44630.2 (Oryza sativa), 5'ss of exon 3
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgtatatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattg-gtaaagtgattgagctg---
||  || |||||||||||||| |||||||| ||  | || |||||||| ||  |||| || |||||||||||||| |||||||| |||||||||||||| |||||||| ||    || | |  |  |    | || ||   |||  ||  ||  ||    ||  | || |   || |  | || |  || | ||| | |     
TGACGGTCTTGGTGCTGAGATTGTTGGCACCTTCATCCTGGTCTACACCGTCTTCTCAGCCACTGATGCCAAGAGGAATGCCAGGGACTCACATGTTCCTgtaagtatccttctcctttttgca-gtgtg-atatgtgaaagttcagtagtagttagt--gtggtctaatgagttatgcactgtgataactaattcatcaccaa

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 2
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgtatata-tacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaagtgattgagctg
|| ||| ||||| |||||||| |||||||| ||  | || |||||||| ||  |||| || || ||||||||||| |||||||| ||||| |||||||| ||||||| |||  | ||     | |  ||  |   |  || | | | ||| | | |   |   | |   ||         ||  ||||    ||  |  | 
TGATGGCCTTGGCGCTGAGATTGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCAGCCACCGATGCCAAGAGGAATGCCAGGGACTCCCATGTTCCTgtaagtactcttccacttcccttttcctagtttgttcagttgttatagttctgcttggattagtttggcttagcacacatatatgtaattgaatcaactt-

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G01860.1 (Glycine max), 5'ss of exon 2
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgtatatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaagtgattgagctg----------------------
|| ||| ||||| |||||||| |||||||||||||||||||||||||| ||| ||||||| ||||||||||||||||| || |||||||| || ||||| ||| ||||||| || |  |  |    | | ||   ||     |  | |  |  |||  | | |||||  |   ||   ||||  |   || | ||                           
TGATGGACTTGGAGCTGAGATTGTTGGCACTTTTGTTCTTGTCTACACCGTTTTCTCTGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCTgtatgtattctttcccactacaatattgcttattcattccactaatttggtttataaatggctatattctgactttgtaattaatgtggttaatgtatgatgctatgatataataattgtag

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G37730.1 (Glycine max), 5'ss of exon 2
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaag-tattctctctctgtgtatata-tacataaatatgtgggtttt----gttttacatatctagttatatat-ttctttgtcaattggtaaagtgattgagctg-------------------------
|| ||| ||||| |||||||| |||||||||||||||||||||||||| ||| ||||||| ||||||||||||||||| || ||||||||||| ||||| ||| | ||| |||| ||  | |    | ||||  | |   |   ||       |||  | |||  |    ||||| ||||   |   ||  ||| ||| || |  |                          
TGATGGACTTGGAGCTGAGATTGTTGGCACTTTTGTTCTTGTCTACACCGTTTTCTCTGCCACTGATGCCAAGAGAAACGCTAGAGACTCACACGTTCCTgtatgctatactctttccttttccccactacaatattgcattcattccattaatttggcttataaatgagtatatattctgactttgttattaatgtggttaatttatgatggtatgatataataattgtag

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgta-tatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaagtga--ttgagctg
|| ||| ||||| || ||||| |||||||||||| ||||||| ||||||||  |||| || ||||||||||||||||| || |||||||| || || || |||  ||||     ||| | |  | | | |  |    ||    |||      |  | | ||   | |  ||| || |  |  | | | || ||   | | || 
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaa--acaggtttattagctaggtagaagagagagactaaact-

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc-tctctctgtgtatatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaag-tgattgagctg
|| ||| ||||| |||||||| |||||||| ||| ||||||| ||||| ||  |||| || ||||||||||||||||| || |||||||| || ||||| |||   |||| ||    |   | | | | |  |  | ||    |||      |  | | ||   | |  ||| || |  |  | | | || | |     || 
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaa--acaggtttattagctaggtagaagagataaactcacta

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ18960 (Selaginella moellendorffii), 5'ss of exon 2
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgtatatatacataaatatgtgggttttg---ttttacatatctagttat-atatttctttgtcaattggtaaagtgattgagctg-------------------------------------------------------------------------------------------
 | ||| ||||| |||||||| ||||| || || ||||| |||||||| ||  |||| || |||||||||||||||| |||||||||||| ||||| || ||| || |  |||  |     |    |   |  ||       |  ||   |||| | | |||  || | || ||  | |||   ||    |  |  |   ||||                                                                                           
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACGGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgtttcttcttccatccaaagctttggttgattcccctctcatgaagttttgcttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ11572 (Selaginella moellendorffii), 5'ss of exon 2
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgtatatataca-taaatatgtgggtttt-----gttttacatatctagttat-atatttctttgtcaattggtaaagtgattgagctg-------------------------------------------------------------------------------------------
 | ||| ||||| |||||||| ||||| || || ||||| |||||||| ||  |||| || |||||||||||||||| |||||||||||| ||||| || ||| || |||||  ||  |  | |  |    |  ||       | |      ||||||| | |||  || | || ||  | |||   ||    |  |  |   ||||                                                                                           
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgt-ttctccttccatccaaagctttggttgattcccccctctcatgaagttttacttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

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|351014038|gb|FQ434190.1|FQ434190
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|351039371|gb|FQ461238.1|FQ461238
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|351047812|gb|FQ459032.1|FQ459032
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|110702772|gb|EE079034.1|EE079034
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCTGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|349818459|gb|FQ401073.1|FQ401073
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTCTGCAGTGTTCTTGGTTCATCTGGC-
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|349814380|gb|FQ398820.1|FQ398820
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGGC
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGG-C
EST: gi|351048846|gb|FQ449714.1|FQ449714
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCTGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|110699569|gb|EE076680.1|EE076680
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCTGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|349833149|gb|FQ416527.1|FQ416527
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTC
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTC
EST: gi|351047271|gb|FQ454882.1|FQ454882
EST:     TCTCTCCTGCA-CTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCCGAT-GGGTTTGC
genomic: TCTCTC-TGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCC-GATTGGGTTTGC
EST: gi|77584848|gb|DV221502.1|DV221502
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGG
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGG
EST: gi|351026354|gb|FQ428366.1|FQ428366
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|349811111|gb|FQ406123.1|FQ406123
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTTGGC
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCT-GGC
EST: gi|351056171|gb|FQ453633.1|FQ453633
EST:     TTCTCTCTGCAACCGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|349829907|gb|FQ422220.1|FQ422220
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCTTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA
EST: gi|351012484|gb|FQ427085.1|FQ427085
EST:     TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCA                         ATTTTGGCTCCTCTCCCGATTGGGTTTGCTGTGTTCTTGGTTCATCTGGCA
genomic: TTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc ... tgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgtatatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaagtgattgagctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtaaag