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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgttgctatcttctagctccattcttttgggcaagacagataacagtttcatccatgctaattggtggtatttctattagggt...

Basic information

species Vitis vinifera
transcript Vv13s0073g00170.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 7
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgttgctatcttctagctccattcttttgggcaagacagataacagtttcatccatgctaattggtggtatttctattagggt-----
| || || |||||||| |||||  | || |||  |||   |||||||||||| ||||||||||| ||||||||||| || ||||| || ||  | ||||||||||  |       |   ||  |||     |  | |||     ||    |  |  | | || |   ||    |  |  |  |||||     ||   | |     
AGGAGGCTGTTGAAAAGGATGCTTCGAAGACTATTGTTAATGATGGAACTGTGCATCCTTTGACTAGCTATGTGATTAATTATGTTAAATTCTTATTTGAgtaagtactcacttttaacttagtattc---aaattcatggacatgta-gattcgtaaatcactacaatttgagtgaggta-tggtacaatgatcgcgatgagta

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgt-tgctatcttctagctccattcttttgggcaagacagataacagtttcatccatgctaattggtggtatttctattagggt---
||||||| |||||||| || |||||||| | |  |     |||||| || || ||||||||||| ||||| ||||| |||||||| || ||| | ||||||||||    | |||   |||   ||   |  |  ||  | | |  | |            | | |||| | |||      |       | || |  ||  |   
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagta--tatgatcatgtgcacttaatctttcctgtaatttgatagttgcattg--ctatactttcttgcatttcttcttcaatcctatccaccagtatgct

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G074530_T01 (Zea mays), 5'ss of exon 1
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgttgctatcttctagctccattcttttgggcaag-acagataacagtttcatccatgctaattggtggtatttctattagggt---
||||||| |||||||| ||||||||||| | |  |    |||||||||| ||||||||||| ||||||||||||||||||||||| |||||| | ||||||||||    ||| |     |    ||    |   |   || || |     |  |    ||  || ||  ||| |    ||  |||   || || ||    |   
AAGAAGCTGTTGAAAAGGATGCAACAAAGAATATTCATACTGATGGAACAGTTCATCCTTTAACAAGCTATGTGATCAACTATGTTAAGTTTTTGTTTGAgtaagta--tctaatcaaatccgcatgcaatttatgtgttgttataaatgaataggtgtacaagatttgtccttatccat--gtgcctttccttttctaattat

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 7
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctg-actgtgttgctatcttctagctccattcttttgggcaag--acagataacagtttcatccatgctaattggtggtatttctattagggt
||||||||||||| |||||||| ||||| ||||| ||  ||||||||||||| ||||||||||||||||||||||| ||||||||||||||| | ||||||||||  | | |   |||| ||    |       ||| |      |    |||  |    || || | |      |  |||||||||  |   ||        
AAGAAGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACTGATGGAACTGTCCATCCTTTGACAAGCTATGTGATTAACTATGTGAAGTTTTTATTTGAgtaagttcatttctgctgtattctgcttcaaattctcgagcgcactcatgaagttatgtctagcattgtatattgttttaattggtgagaaagctgcgtc---

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G17500.1 (Glycine max), 5'ss of exon 4
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgttgctatcttctagctccattcttttgggca-agacagataacagtttcatccatgcta-attggtggtatttctattagggt------
||||||||||||| |||||||| ||||| ||||| ||  ||||||||||||| ||||||||||||||||||||||| ||||||||||||||| | ||||||||||  | | ||       |||| | |||| ||| ||   | |    || |  ||   |    | ||   |||  || |||| |   |||  |   |  |       
AAGAAGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACTGATGGAACTGTCCATCCTTTGACAAGCTATGTGATTAACTATGTGAAGTTTTTATTTGAgtaagttcatatg-------tgctgtattct-gcttcaaattctcaaccacacccatgaagttatctctagcattgtatattgttttcattggtgaaaaagctgcatc

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 7
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgttgctatct---tctagctccattcttttgggcaagacagataacagtttcatccatgctaattggtggtatttctattagggt-
|||| |||||||| |||||||| ||||| ||||| ||  | ||||||||||| |||||| | ||||||||||| || ||||||||||||||| | ||||||||||  |      || |||||  ||||    | |  |   |          |  |    || || |||   |  || | | || ||  |    | ||||    
AAGAGGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACAGATGGAACTGTCCATCCTCTAACAAGCTATGTAATTAACTATGTGAAGTTTTTATTTGAgtaagttc----agctatgttgtcatctgatcccaattttgtagccgcatcaattatttctagcattttttgctgtgttcactgatgacaaaaatgttagtcat

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 7
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgttgctatct---tctagctccat--tcttttgggcaag-acagataacagtttcatccatgctaattggtggtatttctattagggt
|||| |||||||| |||||||| || || ||||| ||  | ||||||||||| |||||| | ||||||||||| || ||||||||||||||| | ||||||||||  |      || |||||  ||||    | |  |   |   | |     |||  |    || || |||   |  || | | || ||  |    | ||||   
AAGAGGCAGTTGAGAAAGATGCTACGAAGACTGCAGTAACAGATGGAACTGTCCATCCTCTAACAAGCTATGTAATTAACTATGTGAAGTTTTTATTTGAgtaagttc----agctatgttgtcatctgatcccaattttgtagccataccatcaattatttctagcattttttgctgtgttcactgatgacaaaaatgttagt--

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctc----tgactgtgttgctatcttctagctcc------attcttttgggcaagacagata-------acagtttcat-ccatgc--taattggtggt-atttctattagggt
||||||| ||||| |||||||| ||||| ||||||||    ||||||||||| || ||  | ||||||||||| ||||| ||||| |||||| | || |||||||  | ||      |||    |  | || || | ||        ||| || |   | | || | ||       |  ||  | | ||| ||  |||||| || | |||  | | ||   
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag---

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|46918058|gb|CN547387.1|CN547387
EST:     GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGA                         CTATCAATCAACACTGAAGCAACTCTTTCAAGAATTCGAAAACGAAAAAGA
genomic: GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccct ... atatttacagCTATCAATCAACACTGAAGCAACTCTTTCAAGAATTCGAAAACGAAAAAGA
EST: gi|110363112|gb|EC926682.1|EC926682
EST:     GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGA                         CTATCAATCAACACTGAAGCAACTCTTTCAAGAATTTGAAAACGAAAAAGA
genomic: GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccct ... atatttacagCTATCAATCAACACTGAAGCAACTCTTTCAAGAATTCGAAAACGAAAAAGA
EST: gi|110361233|gb|EC924691.1|EC924691
EST:     GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGA                         CTATCAATCAACACTGAAGCAACTCTTTCAAGAATTTGAAAACGAAAAAGA
genomic: GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccct ... atatttacagCTATCAATCAACACTGAAGCAACTCTTTCAAGAATTCGAAAACGAAAAAGA
EST: gi|71886064|gb|DT035119.1|DT035119
EST:     GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGA                         CTATCAATCAACACTGAAGCAACTCTTTCAAGAATTTGAAAACGAAAAAGA
genomic: GTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccct ... atatttacagCTATCAATCAACACTGAAGCAACTCTTTCAAGAATTCGAAAACGAAAAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgttgctatcttctagctccattcttttgggcaagacagataacagtttcatccatgctaattggtggtatttctattagggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaca