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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagttcttttatttattgtactatggcatttgcaactctactttcatatttttgcctgaaattctatgcttcagcctaataacaagccctttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGGGAATGACTAAGGATGAAGCTGAG

Basic information

species Vitis vinifera
transcript Vv04s0008g02850.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02850.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G08200.1 (Glycine max), 3'ss of exon 5
--cagttcttttatttattgt-actatggcatttgcaactctactttcatatttttgcctgaaattctatgcttcagcctaataacaagccctttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGGGAATGACTAAGGATGAAGCTGAG
     ||  |  ||||||  |  |||     || |||  |    |   ||   |     |    | | | |||   |  || |         ||   |  |||| |||||||||| |||||||||||| || ||||||||||| ||||||||||||||||| |||||||||||||||
tgttatttctaaatttataattgctagcctgttagcattttccttgggatgcatggcttttgtttgcaaagctctggtttacttg---atttttcttttgcagGATCTGGCTCCAGTTACTTGTATGGTTTCTTTGACCAAGCCTGGAAAGAGGGAATGACCAAGGATGAAGCTGAG

upper sequence: Vv04s0008g02850.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G08260.1 (Glycine max), 3'ss of exon 5
---cagttcttttatttattgtactatggcatttgcaactctactttcatatttttgcctgaaattct--atgcttcagcctaataacaagccctttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGGGAATGACTAAGGATGAAGCTGAG
      ||  |  ||||||  |    | || | |     | | | ||   ||   || ||    ||    | |||   |     | |   | | |||     |||| ||||| |||| |||||||||||| || ||||||||||| ||||||||||||||||| ||||||||||| |||
ttattatttctaaatttatcattgc-tagcctgttagctttttccttgggatgcatggcttttgtttgtaaagctatggttacttgatttgtctttt----gcagGATCTGGGTCCAGTTACTTGTATGGTTTCTTTGACCAAGCCTGGAAAGAGGGAATGACCAAGGATGAAGCCGAG
















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|30255565|gb|CB971697.1|CB971697
EST:     TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAG                         GTTCTGGCTCCACTTACTTGTATGGATTTTTCGACCAAGCATGGAAAGAGG
genomic: TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAGgtatttttgt ... ttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG
EST: gi|110364685|gb|EC928117.1|EC928117
EST:     TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAG                         GTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG
genomic: TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAGgtatttttgt ... ttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG
EST: gi|30255645|gb|CB971777.1|CB971777
EST:     TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAG                         GTTCTGGCTCCACTTACTTGTATGGATTTTTCGACCAAGCATGGAAAGAGG
genomic: TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAGgtatttttgt ... ttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG
EST: gi|32457706|gb|CD798880.1|CD798880
EST:     TGCAATCCCTCTTGGAGGCACAATTATAGAGCAGCCTTTTGCTATTGGAG                         GTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG
genomic: TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAGgtatttttgt ... ttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG
EST: gi|37184119|gb|CF603473.1|CF603473
EST:     TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAG                         GTTCTGGCTCCACTTACTTGTATGGATTTT
genomic: TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAGgtatttttgt ... ttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTT
EST: gi|110373857|gb|EC938261.1|EC938261
EST:     TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAG                         GTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG
genomic: TGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTTTTGCTATTGGAGgtatttttgt ... ttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttttgcctgaaattctatgcttcagcctaataacaagccctttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGGGAATGACTAAGGATGAAGCTGAG
                               taataac  putative branch site (score: 1)
                                         ccctttcatc  putative PPT
             aaattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagttcttttatttattgtactatggcatttgcaactctactttcatatttttgcctgaaattctatgcttcagcctaataacaagccctttcatcacagGTTCTGGCTCCACTTACTTGTATGGATTTTTTGACCAAGCATGGAAAGAGGGAATGACTAAGGATGAAGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagcc