Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttctcgggtattttattttaattactctattaattctgtcttgcgtgacttatgaatttaaatagcctaaagcttaatcaacttattgatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGAGGAATTCTGCAAATCGAGCTGTTGGGTAGAGTTCAGAAACAAGAGATGG

Basic information

species Vitis vinifera
transcript Vv16s0100g00510.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G26950.2 (Glycine max), 3'ss of exon 4
atgttctcgggt------attttattttaattactctattaattctgtcttgcgtgacttatgaatttaaatagcctaaagcttaatcaacttattgatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGAGGAATTCTGCAAATCGAGCTGTTGGGTAGAGTTCAGAAACAAGAGATGG
   || | ||||      |  | ||||| |||  | ||  ||| | || ||   || ||| ||  |   | | |    ||| |  |   || || |||    ||||||||||||||||||||| ||||||||||| ||||||| ||| |||||||||||  | |||| | | |||||||||||||||||||| |||||||| ||||
--ctttttgggtggagtgacctcatttttatttttttac-aatacagtattttatg-cttgtgtttgacacttgaaataagtt--agtgacatactgactttacagGAAAACCGCTTGCAAAAATTCAAGCTACCTGAACCTGTTCTGTGCATTGGAGGTGTACTGCTAGTTGAGCTGTTGGGTAGAGTTCAAAAACAAGAAATGG

upper sequence: Vv16s0100g00510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G32240.1 (Glycine max), 3'ss of exon 3
-atgttctcgggtattttattttaattactctattaattctgtcttgcgtgacttatgaatttaa-atagcctaaagcttaatcaacttattgatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGAGGAATTCTGCAAATCGAGCTGTTGGGTAGAGTTCAGAAACAAGAGATGG
 ||    |   | |||  |  |  |||  | | || |   |    |     |   |||  ||| | |    | | || ||| |  || || |||    ||||||||||||||||||||| ||||||||||| ||||||| ||| |||||||||||  | |||| | | |||||||||||||||||||| || ||||| ||||
tatccattttag-attgaaaatgtatttttttttttacaatacagtattctatgcatgtgtttgacacttgcaataggttagt-gacatactgactttacagGAAAACCGCTTGCAAAAATTCAAGCTACCTGAACCTGTTCTGTGCATTGGAGGTGTACTGCTAGTTGAGCTGTTGGGTAGAGTTCAAAAGCAAGAAATGG
















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|30329725|gb|CD012987.1|CD012987
EST:     AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAG                         GAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
genomic: AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAGgtaaagtttt ... gatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
EST: gi|161713363|gb|FC063368.1|FC063368
EST:     AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAG                         GAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
genomic: AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAGgtaaagtttt ... gatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
EST: gi|30251341|gb|CB969074.1|CB969074
EST:     AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAG                         GAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
genomic: AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAGgtaaagtttt ... gatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
EST: gi|30251596|gb|CB969329.1|CB969329
EST:     AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAG                         GAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
genomic: AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAGgtaaagtttt ... gatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
EST: gi|30251190|gb|CB968923.1|CB968923
EST:     AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAG                         GAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
genomic: AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAGgtaaagtttt ... gatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
EST: gi|30330320|gb|CD013582.1|CD013582
EST:     AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAG                         GAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
genomic: AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAGgtaaagtttt ... gatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
EST: gi|30251256|gb|CB968989.1|CB968989
EST:     AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAG                         GAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA
genomic: AGGATCAGTACATATGGACATATACTTCACCAGAGTTCCCAATGGCTCAGgtaaagtttt ... gatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtgacttatgaatttaaatagcctaaagcttaatcaacttattgatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGAGGAATTCTGCAAATCGAGCTGTTGGGTAGAGTTCAGAAACAAGAGATGG
                                         tattgat  putative branch site (score: 3)
     acttatgaatttaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttctcgggtattttattttaattactctattaattctgtcttgcgtgacttatgaatttaaatagcctaaagcttaatcaacttattgatgaaacagGAAAACCGCTTGCAAAAGTTCAAGCTACCAGAACCTGCTCTTTGCATTGGAGGAATTCTGCAAATCGAGCTGTTGGGTAGAGTTCAGAAACAAGAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatagc