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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgttattgttctcttttatattacgtgaactctttcctcccttggtacaaaatttggtactttaatatcggtattag...

Basic information

species Vitis vinifera
transcript Vv11s0052g01710.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G081682_T01 (Zea mays), 5'ss of exon 10
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgttattgt-tctcttttatattacgtgaactctttcctcccttggt-acaaaatttggtactttaatatcggtattag
 || || ||  ||||||| ||||||||||| |||||||||||  |||| ||||| ||||||||  |||| || ||||||   ||||| ||||| ||| |||||     || ||   |   |   | |  ||| ||||   | || |  |||  |   ||      ||| |  |   |||||    |  |             
CACTCACTACCTAGGTGGTGAAAACTATGTGTTCTGGGGTGGAAGAGAGGGTTACCAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTGgtatga--atggggtttatttgccgattctgtgtctcagctttactttgtggccaaattatctgattgtttgctggatttg----tccag------------

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G313536_T01 (Zea mays), 5'ss of exon 9
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgttattgttctcttttatattacgtgaactctttcctcccttggt-acaaaatttggtactttaatatcggtattag
 || || ||  ||||||| ||||||||||| |||||||||||  |||| ||||| ||||||||  |||| || ||||||   ||||| ||||| ||| |||||     || ||   |   |   | |  |||  |   || || |  |||  |   ||      ||| |  |   |||||    |  |             
CACTCACTACCTAGGTGGTGAAAACTATGTGTTCTGGGGTGGAAGAGAGGGTTACCAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTGgtatga--atggggtttatttgccgattctgtcttagctt-tactttgtggccaaattatctgattgtttgctggatttg----tccag------------

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G544990_T01 (Zea mays), 5'ss of exon 9
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgttattgttctcttttatattacgtgaactctttcctcccttggt-acaaaatttggtactttaatatcggtattag
 || || ||  ||||||| ||||||||||| |||||||||||  |||| ||||| ||||||||  |||| || ||||||   ||||| ||||| ||| |||||     || ||   |   |   | |  ||| ||| | | || |  |||  |   ||      ||| |  |   |||||    |  |             
CACTCACTACCTAGGTGGTGAAAACTATGTGTTCTGGGGTGGAAGAGAGGGTTACCAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTGgtatga--atggggtttatttgccgattctgt-ctcatctttactttgtggccaaattatctgattgtttgctggatttg----tccag------------

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 10
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgttattgttctcttttatattacgtgaactctttcctcccttggtacaaa--atttggt-actttaatatcggtattag
 || || ||  ||||||| ||||||||||| || ||||||||  |||| ||||| ||||||||  ||||||| ||| |    ||||| ||||| ||||||||||    | |||    |  ||||||| ||    || ||| | |  |      |  ||       ||| |||||  ||||| | |||||  | |  | |    
CACTCACTACCTAGGTGGTGAAAACTATGTGTTTTGGGGTGGAAGAGAGGGTTACCAAACTCTTCTGAACACTGATCTTAAGAGAGAACTTGACCATTTGgtacg---agtggg-gcctattttgttgtt----tcctttgtgtctc------tgctttactttgtggcacaaattatttgctcactttcttttgtgcag---

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA17G07380.1 (Glycine max), 5'ss of exon 10
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattg-gacatccgttttgttattgttctcttttatattacgtgaactctttcctcccttggtacaaaatttggtactt-taatatcggtattag
 ||||||||||| || |||||||| |||||||||||||||||||| |||||||||||| |||| ||||||||||||||||   |||||||| |||||||||| | |  ||   |    || |   |||||||||    |||    | | |    | |||| |   |   || | |||||   |    |  | | |  |||| 
GACACATTATTTGGGGGGAGAAAATTATGTTTTCTGGGGTGGTCGTGAAGGTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaatcatggttgccttgaagttattgtttgactttgc--tgccttttttatttcttgtataactaaacaatttataagaaatcttcttgaaattaa

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgtt---------attgttctcttttatattacgtgaactctttcctcccttggtacaaaatttggtactttaatatcggtattag--------------------
                                                    ||||| || || |||||||| |||||||||||||||||||||||| | |     || || ||      | ||| |         |   ||   ||  |   || ||  |||  ||| |    | || |   |||  ||  | |   |    |   |                     
----------------------------------------------------TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctactgcttctttttcttgtcctgtattcagtcttatgggagttattgcacaataatcttctttttatcag

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|351031975|gb|FQ460232.1|FQ460232
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
EST: gi|351032492|gb|FQ458857.1|FQ458857
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
EST: gi|349809734|gb|FQ398359.1|FQ398359
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCCGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
EST: gi|349811710|gb|FQ409707.1|FQ409707
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCCGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
EST: gi|349812955|gb|FQ411195.1|FQ411195
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
EST: gi|351032512|gb|FQ458877.1|FQ458877
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
EST: gi|352786892|gb|FQ481267.1|FQ481267
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
EST: gi|349820047|gb|FQ404769.1|FQ404769
EST:     GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTG                         GCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT
genomic: GTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttat ... ataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgttattgttctcttttatattacgtgaactctttcctcccttggtacaaaatttggtactttaatatcggtattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacaaaa