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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgaaattgtattgatgaggttgcccttcattcttgtcagtattatacttggcaaaatgctgtagtaaattgtttctttacttttctttcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGGGAGCTCATCCAAGTATTGAG

Basic information

species Vitis vinifera
transcript Vv05s0062g01220.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G028004_T02 (Zea mays), 3'ss of exon 7
-ttctgaaattgtattgatgaggttgcccttcattcttgtc---agtattatacttggcaaaatgctgtagtaaattgtttctttacttttctttcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGGGAGCTCATCCAAGTATTGAG
 ||  || ||   |||  |         ||  || | ||||   |  | |  | ||   | ||   | | ||    ||     ||  ||  | ||       |||| || || || |||||||| || |  |||||| | ||    ||||||||||||||||| |||||||||||
atttggatatctaatttgtatcacaaagctagatccatgtcctaaacactgcattta-tagaagattattgttctgtgaacacttgtttcccctt---gtgtagGCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG

upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G44480.3 (Glycine max), 3'ss of exon 7
ttctgaaattgtattgatgaggttgcccttcattcttgtcagtattatacttggcaaaat--gctgtagtaaattgtttctttactttt--ctttcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGGGAGCTCATCCAAGTATTGAG
   |||||   |  |  | |  ||    || || |   ||   ||| || |    || ||    ||||  |  ||| |    ||  ||    || | |||  |||| ||||||||| |||| || |||||||||||| | ||| |||||||||| ||||| || |||||  ||||
---tgaaaaccttatatttaattttttttttatacaaatccacattttattgaataacattaattgta-cagtttgataaaatatgttcaaattgctcaactagGCAATTGAAAAAAGAATTTCTGTCTATTCTCAAATACCAATTGAAAATGGAGAGCTTATGCAAGTCCTGAG
















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|110427318|gb|EC993753.1|EC993753
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349820405|gb|FQ406961.1|FQ406961
EST:     GCTCTGGCATGTTCTTGAGCCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349815347|gb|FQ400502.1|FQ400502
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351036556|gb|FQ457269.1|FQ457269
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351046420|gb|FQ453036.1|FQ453036
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349811155|gb|FQ406107.1|FQ406107
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351056456|gb|FQ454317.1|FQ454317
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCNATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349821182|gb|FQ408769.1|FQ408769
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349807356|gb|FQ401348.1|FQ401348
EST:     GCTCTGGCATGTTCTTGAGCCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351044260|gb|FQ447614.1|FQ447614
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCCATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349817923|gb|FQ407912.1|FQ407912
EST:     GCTCTGGCATGTTCTTGAGCCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351033401|gb|FQ462052.1|FQ462052
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349808011|gb|FQ402402.1|FQ402402
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGA                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351042433|gb|FQ442900.1|FQ442900
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349811066|gb|FQ406054.1|FQ406054
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAAAATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351037271|gb|FQ457104.1|FQ457104
EST:     GCTCCGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|349824801|gb|FQ414659.1|FQ414659
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351032228|gb|FQ460485.1|FQ460485
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTGTTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351049572|gb|FQ429194.1|FQ429194
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351052197|gb|FQ450767.1|FQ450767
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
EST: gi|351055664|gb|FQ452129.1|FQ452129
EST:     GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGG                         GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG
genomic: GCTCTGGCATGTTCTTGAGTCCTGATGACAGCACATATCCAATTGTACGGgtgagtggtc ... tcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacttggcaaaatgctgtagtaaattgtttctttacttttctttcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGGGAGCTCATCCAAGTATTGAG
                          ttgtttctttactttt  CT-rich tract
                      taaattgtttcttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgaaattgtattgatgaggttgcccttcattcttgtcagtattatacttggcaaaatgctgtagtaaattgtttctttacttttctttcgcaatcagGCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGGGAGCTCATCCAAGTATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - -cccttca
- - - - - - - - - - - - - - - - - - - - - - - - - - ggcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgta