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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag

Basic information

species Vitis vinifera
transcript Vv06s0009g03520.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g02530.2 (Oryza sativa), 5'ss of exon 4
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag
||||  | || || |||||||| ||||||||||| || ||||||||||| |||||||| || ||   |||||| ||  | ||||| ||   |||||| | ||| || |   |  |      | ||  |    ||||  |  || || ||| || |||  | |   |   ||   ||  | |  ||      | |||| ||| ||||  |    | ||
TGCTTCTCTCTCTGTTCCTTCTATTCAAGTTTCTCTCGAAAGACTTGGTCAATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaaactct-----ccttggaa--gagctttttcattcatgtaactacttaatactgtatctgtgcaattaagattgttcatgtgc-ttattttttttctgat----gcag

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 4
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag
|||| |||||||| || ||||| ||||||||||| |||||||||||||| || ||||| || ||   |||||| ||  | || || ||  | ||||| ||||| |||| ||   | |   |  |   |   |  | |  |  || || |  | |||||   | | |  |  |   |  || |  | |    ||                        
TGCTTTTATCACTGTTTCTTCTATTCAAGTTTCTCTCAAAAGACTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaggttcattttttttttcttgtaacagctttttcag-acatgtta-agctgtttag---ttgctctactta--tgagtaccgttttatgcag-----------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G044348_T04 (Zea mays), 5'ss of exon 4
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttc------tttccgtatggatcatgctactatgcttaatatttgatataat-tattta-gaaatagtt-tcatgtggtttggttcattatctcacattatctttcttctattttctgtag
|||| |||||||| |||||||| ||||||||||| |||||||| ||||| || ||||| || ||   |||||| ||  | || || ||  | ||||| ||||| || |      | || | | |  |  |||    ||| | |    || || |  | |||||| ||    ||| | |||  |                                           
TGCTTTTATCACTGTTCCTTCTATTCAAGTTTCTCTCAAAAGATTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccattttttctcggaacgtcttttgcagacatgttaagctgtttatgtgctgtatttatgaggccgttcttatgcag-------------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G150251_T02 (Zea mays), 5'ss of exon 4
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag
     |||||||| || ||||| ||||||||||| |||||||||||||| || ||||| || ||   |||||| ||  | || || ||  | ||||| ||||| |||| ||   | |   |  |   |   |  | |  |  || || |  | |||||   | | |  |  |   |  || |  | |    ||                        
----TTTATCACTGTTTCTTCTATTCAAGTTTCTCTCAAAAGACTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCGTAGgttcattttttttttcttgtaacagctttttcag-acatgtta-agctgtttag---ttgctctactta--tgagtaccgttttatgcag-----------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 4
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatg-ctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctc-acattatctttcttctattttctgtag
|| | || ||||| ||| | ||||||||||||||||| || |||||||| ||  ||||| ||||| ||||||||||||| ||||||||  | || ||||||||||||||||   |      || | | | | ||||||  ||||    | | ||    |||    |||||     |||| |   |||| || |||                        
TGTTATTGTCACTCTTCTTACTCTTCAAGTTTCTATCCAAGGACTTGGTGAACACTGTATTGACAGGCTACTTCTTTGTACTTGGGATTGTTGCCCTTTCgtatgttctttttct------cacgtccaatgtgcttatcatttcgagtcaata----gaatctttttcaacatatttgctattttatgtctacag-----------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G08620.3 (Glycine max), 5'ss of exon 4
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgt-atggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctc-acattatctttcttctattttctgtag
|| | || ||||| ||| | |||||||||||| |||| || |||||||| ||  ||||| ||||| ||||||||||||| ||||||||  | || ||||||||||||||||||   |||    |||    | |  || | |||  ||| |||  |||        ||| |     |||| |   |||| || |||                        
TGTTATTGTCACTTTTCTTACTCTTCAAGTTTTTATCTAAGGACTTGGTGAACACTGTATTGACAGGCTACTTCTTTGTACTTGGGATTGTTGCACTTTCgtatgttctttcctccatgcccaatgtgcttgtcatttagattcaatagaatatttt--------ttttaacatatttgctattttatgtctacag-----------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag
||||  | ||||| ||| |  | ||||||||||| ||||| ||||||||||||||||| || |||   ||||||||||| ||||||||  ||||||||||||||||  | ||    |  |||||||   |    ||  |||||| | ||  | |    || |  |  || |  |||  ||   ||  |                             
TGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGGTTAATGCTGTGCTAACAGCTTACTTCTTTGTTCTTGGGATTGTCGCTCTTTCgtatgtcttatc----taaatcatgccttttgtttttttatttgtt-tatctgtggtcaagtcatgacacg--gttatgtgtgtttgcag---------------------------

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|71877015|gb|DT026070.1|DT026070
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|27579299|gb|CB001994.1|CB001994
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|351030693|gb|FQ438531.1|FQ438531
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|22010806|gb|BQ795840.1|BQ795840
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|77579348|gb|DV218502.1|DV218502
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|161717568|gb|FC066896.1|FC066896
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|349812621|gb|FQ409780.1|FQ409780
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|110730433|gb|EE107509.1|EE107509
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|110708740|gb|EE086629.1|EE086629
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
EST: gi|71874644|gb|DT023699.1|DT023699
EST:     AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTC                         GGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA
genomic: AATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctt ... ttttctgtagGGCAACATTGCTACCTGCAATTAGACGTTATTTGCCAAAGCATTGGAATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG