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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagcaaaaaatttaataacctgtctgatcttaattatttttcctataagtgactattctcttttatgtagatgctaattggttactcatagttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG

Basic information

species Vitis vinifera
transcript Vv13s0019g03960.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G31830.1 (Glycine max), 3'ss of exon 6
ctagcaaaaaatttaataacctg--tctgatcttaattatttttcctataagtgactattctcttttatgtagatgctaattggttactcatagttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG
||| ||  ||||   ||     |  ||||||     |||||||    ||      ||   || ||| ||| | |  ||||    |   | || ||||| ||||| ||||||||||| |||||| | ||||| |||| ||| ||  | ||| | ||| ||||||| |||||||||||||||
ctatcatgaaatactatggttgggttctgattcgtcttattttaaa-atctacatctcgactttttaatgaaaagactaagatttatttaattgtttt-cagGAAGAATGCAAACGTGTATCAACTGAGGGGCAAAACTTAAGGCTGGACTTGTCAGCCAAGTTTCAAGATGCAATCAAG
















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|352782197|gb|FQ470099.1|FQ470099
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|351029666|gb|FQ427506.1|FQ427506
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAAATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|351025048|gb|FQ433465.1|FQ433465
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|110711711|gb|EE088504.1|EE088504
EST:     AGCTTGAGTCACTGTGTANGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTTGAGAT-AGACCT
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTT-GAGATTAGACCT
EST: gi|30255027|gb|CB971474.1|CB971474
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|352769260|gb|FQ471409.1|FQ471409
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCCGAACAAATTGCTAATG                         GATGAATGCAAA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAA
EST: gi|110713047|gb|EE088636.1|EE088636
EST:     AGCTTGAGTCACTGTGTANGGAATTA-AACGTCAGAACAA-TTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAA-CCTTGAGATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|351023970|gb|FQ423393.1|FQ423393
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|30254970|gb|CB971417.1|CB971417
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|110721939|gb|EE097735.1|EE097735
EST:     AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGCAAACGAGTATCAGCAGAAGGCCAAACCTTGAGATTAGACCTA
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTA
EST: gi|110711601|gb|EE088266.1|EE088266
EST:     AGCTTGAGTCACTGTGTAGGNAATTACAACGTCAGAACAAATTGCTAATG                         GATGAATGNCAA-CGAGTATCAGCAGAAGGCCCAACCTTGAGAATAGACCT
genomic: AGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATGgtgtgctttc ... agttttgcagGATGAATG-CAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagtgactattctcttttatgtagatgctaattggttactcatagttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG
                           tgctaat  putative branch site (score: 2)
                ttttatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagcaaaaaatttaataacctgtctgatcttaattatttttcctataagtgactattctcttttatgtagatgctaattggttactcatagttttgcagGATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - -aaaaaat
- - - - - - - aataacc
- - - - - - - - - - -tgtctga