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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttctttagcgttaaaatatttataatatttagtagaaacatattttgggaaatattttgtgtattgataataaatatatgttggaatctactat...

Basic information

species Vitis vinifera
transcript Vv00s0233g00060.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0233g00060.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os04g55060.1 (Oryza sativa), 5'ss of exon 5
TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttctttagcgttaaaatatttataatatttagtagaaacatattttgggaaatatt-ttgtgtattgataataaatat---atgttggaatctactat--
||| || ||||| || ||||||||||| |  | ||| |||||||| || ||||| || || || |||||||| ||||||||||||||| |  ||||||||||| |  |   |   | | ||||||  ||| |  ||   |      |||      || ||||  |  ||| | |  || |   |   ||| |  | |    | |  
TCTAGTAATTGGTGCCGATGCTCTTTCACAATTTGTGGATTGGACAGACAGAGGTACATGCATCCTCTTTGGTGATGCTGCTGGTGCTGTTTTGGTTCAGgtatttgttacttttgctgaaatatcgata-tgctttccac-----tatccaccaaattattactccgtactaagtatgagcgtcccatgcttaagttggttttca

upper sequence: Vv00s0233g00060.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA09G41380.1 (Glycine max), 5'ss of exon 5
TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttctttagcgttaaaatatttataatatttagtag-aaacatattttgggaaat---attttgtgtattgataataaatatatgttggaatctactat
||| || ||||| || ||||||||||| || |||||||||||||| || ||||||||||||||||| ||||||||||||||||||||| |||| || |||||| |  | | || | |  |   |||  | |   || |||| |||  |   || | || |   || |||| | |||   || |  ||  |||    |    || 
TCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGCTGGTGCTGTACTAGTACAGgtaat--tgtatatcttccaggcattgttcaacattggtagcaaatgtcagttagcaatttggatcttgtttcttggctattacaattagttttg-ttggtta-

upper sequence: Vv00s0233g00060.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA18G44350.1 (Glycine max), 5'ss of exon 5
TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttctttagcgttaaaatatttataatatttagtagaaacatattttgggaaat---attttgtgtattgataataaatatatgttggaatctactat
 || || ||||| || |||||||| || || |||||||||||||| || ||||||||||||||||| ||||||||||||||||||||| |||| || |||||| |  | | |     |   || | |  ||| |||     |||  |    | | || |   || |||| | |||   || |  ||  |||    |    |||
-CTAGTTATTGGGGCGGATGCTCTCTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGCTGGTGCTGTACTAGTACAGGtaattgtatatcttcctggcat-tgtccaatgtttgtagcaaatgtcagctagcaatttggatcttgttttttggctattacaattagttttg-ttggttat

upper sequence: Vv00s0233g00060.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G00550.1 (Glycine max), 5'ss of exon 4
TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtag--tgttctttagcgttaaaatatttataatatttagt------agaaacatattttgggaaatattttgtgtattgataataaatatatgttggaatctactat
||| || |||||||| |||||| |||| || |||||||||||||| ||||||||  |||||||||| |||||||||||||| ||||||  ||| || ||||||   |||   |   | |      ||| |||  |  | ||       | ||  ||| |      ||   || ||    |  | ||    || |||| |         
TCTAGTCATTGGAGCCGATGCTATTTCACGATATGTTGATTGGACAGATAGAGGCTCCTGTATTCTTTTTGGGGATGCTGCCGGTGCTGAACTAGTACAGgtaaattgtatatcttcctgcggccattcatagcaaattgtcaagttggcaaggtatataaatcgatgcctt-tgctcaggaactatgattacgttgcag--------

upper sequence: Vv00s0233g00060.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G62640.2 (Arabidopsis thaliana), 5'ss of exon 6
TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttctttagcgttaaaatatttataatatttagtagaaacatatt-----ttgggaaatattttgtgtattgataataaatatatgttgg-aatctactat--------------------------------------------------------------------------------------------
| | ||||| ||||||||| || | ||||| | |||||||||||| ||||||||||| || ||||| ||||| ||||||||||||||| |  | ||||||||| ||| | |||    | ||   |||     |||| ||  |   ||||      || | | | ||    |  ||||| |    |||    || | ||  || ||                                                                                             
TTTAGTGATCGGAGCTGATTCTTTGTCTCGGTTTGTTGATTGGACGGATAGAGGGACTTGCATTCTATTTGGAGATGCTGCTGGTGCTGTGGTTGTTCAGgtactgtgcctta----tgaagcttttgagcaatttcgtgcacttatatccaaagtttgtatacataagcttcattgaaagagtataacctttagtaaattattacaagtaacacaatcataagacgagtgcttgccacagtgcatatcaaaagatcaatctttgtttattaacgaaatgtcctttcatttcgtgcag

upper sequence: Vv00s0233g00060.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S119_22V6.2 (Physcomitrella patens), 5'ss of exon 7
TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgt--agtgtt-ctttagcgttaaaatatttataatatt-tagtagaaacatattttgggaaatattttgtgtattgataataaatatatgttgga-atctactat----------------------------------------------------------------------------------------------
 |||||| | || || |||||||| || || || || ||||||||||| |||||||| |||||||| ||||| |||||  |||| ||  | ||  | |||||    || | ||| ||   ||  | |    | ||  |       |||       |   || | |||||  | |     |  ||     ||     |||| |                                                                                                 
ACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTCTGGAGCGCTTCTTTTACAGgtctgttgctacttaagttctaggaaaaacttgatgctactacttaaatgaccactaaaaacttttttgcctctcacccagtaacgccagtcaatcatcttcgggttgtcgaggttgtaggtgctacatcatcatgagccgcgtatgtgatatttcatttcaatcgtatcgctaatattttgcggtcctctttcaacag

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|110691846|gb|EE070412.1|EE070412
EST:     GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAG                         GCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGTGAT
genomic: GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttct ... cattctgcagGCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGTGAT
EST: gi|110426428|gb|EC992837.1|EC992837
EST:     GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAG                         GCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGTGAT
genomic: GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttct ... cattctgcagGCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGTGAT
EST: gi|110413417|gb|EC979202.1|EC979202
EST:     GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAG                         GCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGTGAT
genomic: GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttct ... cattctgcagGCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGTGAT
EST: gi|110372425|gb|EC936588.1|EC936588
EST:     GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTGTACTGGTTCAG                         GCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGCGAT
genomic: GAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttct ... cattctgcagGCCTGTGATAGTGAACAAGATGGTTTATTTGCTTTTGACTTGCATAGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGCTGGTGCTATACTGGTTCAGgtagtgttctttagcgttaaaatatttataatatttagtagaaacatattttgggaaatattttgtgtattgataataaatatatgttggaatctactat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataataaa