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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag

Basic information

species Vitis vinifera
transcript Vv14s0083g00540.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 4
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttga----aatgcag
|||| |||||||||| ||||||||||| || || ||||| ||| | || |||||| | || ||||||||||| ||||| || ||||||||||| || ||||||||  |   |  |  || |  | | ||    |      || |    |  ||| | | ||  | |   | | |  | |     ||||||
ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactg-ctgactagttttaggatataaacttattc--tgttgagtaatatgtgttctcttttgcataatcatgatgcag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 4
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatact----gaatgacattggattg---gtatcgtttgaaatgcag
 ||| | ||||| || || || ||||| || || ||||| ||  | || ||  ||||||| ||||| ||||| |||||||| |||||||||||||| ||||||||    |  ||  |    | ||   | | || |  | | | | |||       |||| | |||  ||||     |   ||     |||||
TCATATATTCTTTCAACAAAGGCATGGTCCAGGCCAAAGATCATTGTATAACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttg----ttttgagttcggtgacctattttttca--gatagaaagatctctctggaataatattctattgtttacacaattcattttgcag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G07090.1 (Glycine max), 5'ss of exon 3
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag
|||||| |||||||| ||||||||||||||||| ||  ||||||||||||||||| | || || |||||||| | |||||||||||| || |||||||||||||    |||| | | | ||||||  |||| |   ||  ||  |   || |  || | |||| ||   |    ||  || | |||
ACATGTATTCTTCCAACAGAGACATGGACCTGGGCAGCGGTCCCTCTACAATGTTCTAAAAGCTTACTCTGTCTTTGACAGAGATGTAGGCTATGTTCAGgtttta--ctcaggaacc-catcacctttctgt--gcttgttacaaagtatttcataatattg-atcatt----ttaaaactacag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA19G05360.1 (Glycine max), 5'ss of exon 4
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag
|||||| ||||| || ||||||||||||||||| ||  ||||||||||||||||| | || || |||||||| | |||||||||||| || |||||||||||||    |||| | | | ||||||  | || |   ||  ||  |   || |  || | ||||       ||  ||  || | |||
ACATGTATTCTTTCAACAGAGACATGGACCTGGGCAGCGGTCCCTCTACAATGTTCTAAAAGCTTACTCTGTCTTTGACAGAGATGTAGGCTATGTTCAGgtttta--ctcagg-accccatcaccttgctgt--gcttgttacaaagtatttcataatattgacc----att-ttaaaactccag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 5'ss of exon 4
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggat--tggtatcgtttgaaatgcag
|||||||||||||||| ||||||||||||| || ||||| ||  | ||||||||| | || ||||||||||| |||||||||||||| |||||||||||||| |   |  ||   ||||  ||  |  |   | |         | | |||| | |   |  |  |  |||||        |||||||
ACATGTTTTCTTCCAGAAGAGACATGGACCAGGCCAAAGATCATTATACAATGTTCTAAAAGCATACTCTGTCTATGACAGAGATGTCGGATATGTTCAGgtat---ttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 5'ss of exon 4
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag
|||||||||||| ||| |||||||||||||||| ||||| ||| | ||||||||  | ||||||||||| || |||||||||||||| |||||||||||||| |       |  ||| ||     | | | ||||    ||  |    ||  | |  |   |  ||   | |  | |    |||||
ACATGTTTTCTTTCAGAAGAGACATGGACCTGGGCAAAGATCCTTGTACAATGTCCTTAAGGCATACTCAGTTTATGACAGAGATGTCGGATATGTTCAGgtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatc---tgcag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S15_13V6.3 (Physcomitrella patens), 5'ss of exon 4
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag---------------
|||||| || |||||||||||||| |||||||| ||| |  | ||||| || ||| | ||||| ||||| || |||||| ||||||| || ||||| |||||  | ||  ||     |||   | | || | |  |   |||  |  ||      |||  |||     || |  | |   ||| |                
ACATGTGTTTTTCCAGCAGAGACACGGACCTGGACAACGAGCTCTCTATAACGTTCTCAAGGCTTACTCAGTTTATGACCGAGATGTCGGTTATGTGCAGgtaggaattgcaaaatgctctcaattgttgtttcaatgctttccattatgtctc-tgagcttgagacagtcttatgttttatgtatgaaggaatttcgtac

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S263_22V6.1 (Physcomitrella patens), 5'ss of exon 4
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgttt-gtaggatactgaatgacattggattgg-----tatcgtttgaa-atgcag-------
 ||||||||||||||||| |||||||| || |||||| || | || ||||||||  | ||||||||||| || |||||| |||||||||| ||||| ||||| |  |||  |  |  |  | ||    | | || | ||| | | |  |||     ||||  | |  | |     ||| | ||    || | |       
GCATGTTTTCTTCCAGCAAAGACATGGGCCGGGTCAACGGGCTCTGTACAATGTCCTCAAGGCATACTCAGTTTATGACCGAGATGTTGGCTATGTGCAGgtataaatccaaaattgcaaaacatctgttttttcaatgtctcgcatcatagaatctgacggtagtgtagacaaatatagcttatttattccgtagaagt

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: EFJ27331 (Selaginella moellendorffii), 5'ss of exon 3
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag
 |||||||||||||||||| | || || ||||| ||  | || || |||||||| |||||||| ||||| || || |||||||||||||| ||||| |||||  |     ||      |  ||||  ||  |   | ||||  || | | ||  || |     ||  |                  
GCATGTTTTCTTCCAGCAGCGGCACGGGCCTGGCCAGCGCTCGCTGTACAATGTCTTGAAGGCTTACTCCGTTTACGACAGAGATGTTGGCTATGTCCAGgtaagagcgaca----ctttctcacgtttggaaacaatgttgttaagctcctcgatcatccatgaccgcag---------------

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: EFJ35318 (Selaginella moellendorffii), 5'ss of exon 3
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag
 |||||||||||||||||| | || || ||||| ||  | || || |||||||| |||||||| ||||| || || |||||||||||||| ||||| |||||  |     ||      |  |||| |||  |   | ||||  ||   | ||  || |     ||  |                  
GCATGTTTTCTTCCAGCAGCGGCACGGGCCTGGCCAGCGCTCGCTGTACAATGTCTTGAAGGCTTACTCCGTTTACGACAGAGATGTTGGCTATGTCCAGgtaagagcgaca----ctttctcacgcttggaaacaatgttgttaatctcctcgatcatccatgaccgcag---------------

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|161719620|gb|FC067048.1|FC067048
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|349829177|gb|FQ419687.1|FQ419687
EST:     ATGTTTTGAAGGCATACTCTGCGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|351012823|gb|FQ430386.1|FQ430386
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|349827061|gb|FQ421334.1|FQ421334
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|349829128|gb|FQ419660.1|FQ419660
EST:     ATGTTTTGAAGGCATACTCTGCGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|351038918|gb|FQ457593.1|FQ457593
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|110417184|gb|EC983219.1|EC983219
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG