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

...tttagaggcaggaatgtggacttctgagggaatttatagggaggcagtaacctctagccttacttctttggtcctaacttcttcgagttttcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01860.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G41580.5 (Glycine max), 3'ss of exon 7
tttagaggcaggaatgtggacttctgagggaatttatagggaggcagtaacctctagccttacttctttggtcctaactt--cttcgagttttcatcta-tagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
 |  |||   |  |  |   || |  |   ||| |   |  |   |  |   | ||    | ||     | || ||   |   ||  |  ||   |||  ||||||||||||||||||||||||||||||||||| ||||| ||
-tctgagtttgtcagtttttctacccacataatattccgtcaa--aacacattttaaaaatgctctacagttcttattgtaattttaaccttctgtcttctagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCGACACAAAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G03820.2 (Glycine max), 3'ss of exon 7
tttagaggcaggaatgtggacttctgagggaatttatagggaggcagtaacctcta--gccttacttctttggtcctaacttcttcgagttttcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
  |         | | |   || ||||   | | |   |  |      |      |  ||  |||   | |  |  ||| ||       || |    | ||||||||||||||||||||||||||||||||||| ||||| ||
--tgagtttgacacttttttctcctgaaatagtattccgtcaaaacacatttaaaaatgctctacagttcttattgtaatttaacaaccttctgtcttgtagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCGACACAAAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G06060.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------------------tttagaggcaggaatgtggacttctgagggaatttatagggaggcagt--aacctctagccttacttctttggtcc---taacttcttcgagttttcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
                                                                                            ||| |       |||     |        | ||||     |    ||      | ||   | | || |||  |||   |||    |   | | | | | |  ||||||||||||||||||||||||| |||||||| ||||||||
gtataaattttggtcatgtggcaaagccctttagactatatgctataattttatttggtgaaaatataacaataagagaaaaccgtcacaccttataaaattttatgccttttctctgaatattttagtttcattttgttttgtttttattgtaaattttttcctccacataaacaataacaatctgc-tttccagGGTGTTGCTGTTGCACTTCCTGTCTATTTTGCGACACAGAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G14090.1 (Glycine max), 3'ss of exon 5
tttagaggcaggaatgtggacttctgagggaatttatagggaggcagtaacctctagccttacttctttggtcctaac--ttcttcgagttttca--tctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
      | |     | |  |  | | ||   | || |     |    |    |  |   ||| || |||      |||  || |   | |||||   |  | |||| ||||||||||| |||||||| |||||||| ||||||||
----atgccttctctctcaatattttagtttaattctgctttgttttttctattgatttttatttttttcacataaacaattatgacaattttctgcttcacagGGCGTTGCTGTTGCCCTTCCTGTCTATTTTGCGACACAGAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------------------------------tttagaggcaggaatgtggacttctgaggg---aatttatagggaggcagtaacctctagccttacttctttggtcctaacttcttcgagttttcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
                                                                                     |||      |  ||     | |   ||||    ||    |||   |    ||   |||    | || |  ||    ||  || || ||   |   || |  |||||||||| |||||||||||| |||||||||||||| ||||
gtagaaattctgtaaccattataaaagatacctagaaagaataacatgtcttatttttcttgcgtgtttcctgtttgactgtctattttccactataaactaatattaaagaggattaaacacctagattgttcata-tttctgatttgacatgctt--ctcttgctgctccggtgtgatattttcagGGTGTTGCAGTTGCACTTCCTATTTATTTTGCAACAGAGAG

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|30251805|gb|CB969538.1|CB969538
EST:     GGGTTGGACTAAACTTGGCANTGGCCATTGCTTTGCACAACATCCCAGAG                         GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
genomic: GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAGgtaggactgt ... tcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
EST: gi|30251808|gb|CB969541.1|CB969541
EST:     GGGTCGGACTATCCTTGGNTCTNGCCATTGCTTTGCACAACATCCCAGAG                         GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
genomic: GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAGgtaggactgt ... tcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
EST: gi|110693804|gb|EE070356.1|EE070356
EST:     GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG                         GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
genomic: GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAGgtaggactgt ... tcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
EST: gi|110689440|gb|EE065664.1|EE065664
EST:     GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG                         GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
genomic: GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAGgtaggactgt ... tcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
EST: gi|110698572|gb|EE076222.1|EE076222
EST:     GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG                         GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
genomic: GGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAGgtaggactgt ... tcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaacctctagccttacttctttggtcctaacttcttcgagttttcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG
                          tcctaac  putative branch site (score: 1)
                                          ttttcatct  putative PPT
                                          ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagaggcaggaatgtggacttctgagggaatttatagggaggcagtaacctctagccttacttctttggtcctaacttcttcgagttttcatctatagGGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -gcaggaa
- - - - - - - - - - cttctga
- - - - - - - - - - - - - - - - - - - -ggaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcttc