Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggttaatgccagaattcaggaa...

Basic information

species Vitis vinifera
transcript Vv02s0012g00910.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 11
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggtta---atgccagaat-tcaggaa-
||||||||||||| |||| |||||||| ||||| ||| ||||||| || ||||  |||||||| || |||| |||||| || ||||||||||||||||||||   |||    |  |  || || ||| |    |     |     | |    |   | | |  | |  ||| |  |||| |||   |      ||| | ||  | 
TGGACAAACTGAGGCAACCATGAGTGCCGAAGTTGAGCTGATTTCTACAATGGGGGAAAAGAAATCATGGAACAGGCCGCCAATTCAGATGGAATTCCAGgt---taattttacctccttttgaacaaccctcttatcattagcaaaatctgtcagccagttcattttatttt--tgagcttacagaaaatgcaatgttagagat

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G331032_T01 (Zea mays), 5'ss of exon 11
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgc--attctgatgaggttaatgccagaattcaggaa-
||| || |||||| |||| ||||| ||||| || ||||||||||| || ||||  ||||||||||| |||| ||| ||||| || ||||||||||||||||||   | | |  |         |  |  | |     ||| | || |    ||| |||| |  ||| |  |    |||  || || |  ||||   |   || 
TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgta---atacacttgcccccaattggaggacacacattttttttgctttattttgtctattgcaattcggaactggatatggatagtagcagagagcttaaat

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA01G40700.1 (Glycine max), 5'ss of exon 11
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggttaatgccagaattcaggaa-
||| ||||||||||||||  ||||||||||||| ||  | |||||||||||| |||||||||| |||||||| || ||||| ||||||||||| || |||||   | |  |  |  |||     | ||   | ||    |   ||  |   | |   | |  |||     |  |   | | | || |  |     |  |  
TGGGCAAACTGAGCCAACCTTGAGTGCAGAAGTTGAACTTATTTCCACGATGACAGAAAAGAAATCTTGGACTAGACCACCAATTCAGATGGAGTTTCAGgtttgttatcagttgctttataacaaattcca-tgaaaatggctggaacattctgattgccttaaaagtataagtgaaagcttattcatgggcatataatt

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA11G04600.2 (Glycine max), 5'ss of exon 7
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggttaatgccagaattcaggaa----
||| ||||||||||||||  ||||||||||| | ||  | |||||||| ||| |||||||||| |||| ||| || ||||| ||||||||||| || |||||     |  |  |  |||     |   ||   ||    |   ||  ||   ||   | |  |||     | ||   | | | || |  |||    |       
TGGGCAAACTGAGCCAACCTTGAGTGCAGAAATTGAACTTATTTCCACAATGACAGAAAAGAAATCTTCGACTAGACCACCAATTCAGATGGAGTTTCAGgtttgctatcagttgctttaacaaattcca---tgaaaatggctgg-aacacttgattgccttaaaagtatttgtgaaagcttattcatgaaaatggttggata

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 5'ss of exon 11
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggttaatgccagaattcaggaa
 || ||||| ||| | ||  | ||||||||| | |||||||| || || |||| ||| ||||| |||||||| ||||||||||| || |||||||| |||||         | | ||| ||| |   |  |    | |  |||  |  |  |||   ||    |||   |  | |     | |         ||    | 
AGGGCAAACAGAGTCCACGCTAAGTGCAGAAATTGAGTTGATCTCAACAATGGGAGAGAAGAAATCTTGGACAAGGCCACCGATCCAAATGGAATTTCAGgtc--------agtctttgtctcttt-taggcactgttaaatagaaccagatttgcttaaagcaat---tattaaccgtctcagctttgttcttttctag

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 5'ss of exon 11
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggttaatgccagaattcaggaa----------------------------------------------------
                                              || ||||  ||||||||||||||||| ||||| || ||||||||||| |||||||| || |     |  |   || |  |  | |  | ||||| |   |      || |||||     ||| |   |||| | | | |     |    | |                                                      
---------------------------------------------AACAATGGTTGAAAAGAAGTCTTGGACGAGGCCTCCCATTCAGATGGAGTTCCAGGTTCCCATGTTTAC-TGCATCCGGCCTACGGGTTCGCTTTTTG-AAGgtccgttctctacccc--tgcctctcgatgtgctaagttttcaatggtatgtgtagatacggtccacagggaattgctcaccttggtgatatttaatttatctag

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|110687469|gb|EE064917.1|EE064917
EST:     TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAG                         GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
genomic: TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaa ... gttcctgcagGTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
EST: gi|110387207|gb|EC951857.1|EC951857
EST:     TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAG                         GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
genomic: TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaa ... gttcctgcagGTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
EST: gi|29782813|gb|CB348455.2|CB348455
EST:     TGGCAGGAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAG                         GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGATTTCG-ATC
genomic: TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaa ... gttcctgcagGTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
EST: gi|32457429|gb|CD798603.1|CD798603
EST:     TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAG                         GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
genomic: TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaa ... gttcctgcagGTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
EST: gi|27582169|gb|CB004864.1|CB004864
EST:     TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAG                         GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
genomic: TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaa ... gttcctgcagGTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
EST: gi|28969506|gb|CB348539.1|CB348539
EST:     TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAG                         GTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG
genomic: TGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaa ... gttcctgcagGTTCCCATGTTTACAGCATCTGGTTTACGCGTTCGGTTTCTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggttaatgccagaattcaggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa