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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtaacagaatagatgacatgttcatgcgtctttgttgaagcttaacatgaaattctcacatttaattttatcaaggcaacatcttccatgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTCAACCTGACAATTGAAGAAGTCAGGTCAAGAGTGTCGAAAGCTCTGGATG

Basic information

species Vitis vinifera
transcript Vv04s0044g01320.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g56400.1 (Oryza sativa), 3'ss of exon 2
----------tagtaacagaata-gatgacatgttcatgcgtctttgttgaagcttaacatgaaattctcacatttaattttatcaaggcaacatcttccatgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTCAACCTGACAATTGAAGAAGTCAGGTCAAGAGTGTCGAAAGCTCTGGATG
            | |   ||  | |||  | |  | |  | |   |||  ||   | | || ||  | ||   |  |    ||| |||  |   ||||  |     ||||||| |||||||| ||||| ||| |||||||||||||||| ||||||||| |||||||  |  | || || || ||||||||||| ||  || | |||||||
ttgactcttgatgcattggaggaagattgcttaatgacacattcatgtcaaa---ttagatcaagctttctggtaca----tattaagttacgttctttgaa----tgcagGTTGTGATGCCGACAGTGGAATCAGATGTTGCATTTGGTCTTGGTAAGCTCAACCTTTCGTTGGATGAGGTTAGGTCAAGAGTATCACAATCACTGGATG

upper sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 3
tagtaacagaatagatgacatgttcatgcgtctttgttgaagct-taacatgaaattctcacatttaattttatcaaggcaacatcttccatgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTCAACCTGACAATTGAAGAAGTCAGGTCAAGAGTGTCGAAAGCTCTGGATG
|||| ||   | |  |   |  |  |    |      |||  |  ||  ||| | |    ||| |     |    |  |      |||  || |  ||||||| || |||||||| |||||  | |||||||||||||| ||||||||| ||||  || |    || |||||||| || || ||||| | |||| || |||
tagtcaccagaaaatttctac-tgaaaatttacagcctgaccccatatgatgtattgtatacaatcggactgtcaactgtgtagccttatatttgttgcagGTGGTAATGCCTACGGTAGATTCTGATGTTGCATTTGGTCTTGGTAAGATCAATTTGGCTCACGATGAAGTCAGATCTAGGGTGTCAAGAGCTTTGCATG

upper sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 2
tagtaacagaatagatgacatgttcatgcgtctttgttgaagcttaacatgaaattctcacatttaattttatcaaggcaacatcttccatgttc--tgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGT-TCA--ACCTGACAATTGAAGAAGTCAGGTCAAGAGTGTCGAAAGCTCTGGATG
| ||      ||    |  |  |   |  ||    |||| |  || |  | || |     |  | | | |  |||   |   |  |||  |||||   ||||||||||||||||||||| ||||| ||||| |||||||| ||||| |||| |||  || |||     |||||||| | ||| || |||   |||||| |||   
ttgttgtcacatctgagggagatcagttagtaacagttggattttgat-tcaagtaaaaccgctcattctggtcacatctgaacgttct-tgttcatcgcagGTAGTGATGCCTACAGTGGAAGCTGATGTGGCATTTGGTCTTGGCAAGTATCATGACATGAATCAGGAAGAAGTTAAGTCTAGGGTGATTAAAGCTTTGG---

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|71870320|gb|DT019375.1|DT019375
EST:     TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAG                         GTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
genomic: TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAGgtcagttttt ... tgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
EST: gi|30136356|gb|CB921694.1|CB921694
EST:     TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAG                         GTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
genomic: TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAGgtcagttttt ... tgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
EST: gi|77579760|gb|DV218758.1|DV218758
EST:     TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAG                         GTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
genomic: TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAGgtcagttttt ... tgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
EST: gi|71870537|gb|DT019592.1|DT019592
EST:     TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAG                         GTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
genomic: TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAGgtcagttttt ... tgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
EST: gi|71875168|gb|DT024223.1|DT024223
EST:     TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAG                         GTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
genomic: TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAGgtcagttttt ... tgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
EST: gi|71866041|gb|DT015096.1|DT015096
EST:     TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAG                         GTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
genomic: TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAGgtcagttttt ... tgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
EST: gi|77581718|gb|DV219803.1|DV219803
EST:     TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAG                         GTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC
genomic: TGTATGTGAAGAAGCCCAAGAGTTTCGTTTTTCAAAATCCCGACCATCAGgtcagttttt ... tgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgaaattctcacatttaattttatcaaggcaacatcttccatgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTCAACCTGACAATTGAAGAAGTCAGGTCAAGAGTGTCGAAAGCTCTGGATG
                                      tcttccat  CT-rich tract
      aaattctcacatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtaacagaatagatgacatgttcatgcgtctttgttgaagcttaacatgaaattctcacatttaattttatcaaggcaacatcttccatgttctgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGTTCAACCTGACAATTGAAGAAGTCAGGTCAAGAGTGTCGAAAGCTCTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - aacagaa
- - - - - - - - - catgttc
- - - - - - - - - - - - - - - - - - -tgaagct
- - - - - - - - - - - - - - - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaggca