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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctgagaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtttgatctgtattagctacctgactagattgtttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG

Basic information

species Vitis vinifera
transcript Vv07s0141g00390.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g06740.1 (Oryza sativa), 3'ss of exon 6
-ccctgagaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtttgatctgtatta-gctacctgactagattgtttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
    | || |          ||  ||||  | ||||  ||||    || ||   ||| ||  |   | ||| | ||| |      |       | ||| |||||||||||||||||| || || ||||| ||||| || ||||||||||||||||||||||| |||
catttcagtatttcactgtttatcagttaaattttatttggtttt-ggttattgttgttccattggatgctccttgattgtgaattgcacaaatttga-cagAGCTGTACCATCTGCCGTTTTCTCCCAACCACCCATCGGACAAGTTGGTCTTACTGAAGAGCAG

upper sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g28000.1 (Oryza sativa), 3'ss of exon 5
ccctgagaaggaagtctaatacaagtttgagttta--aatggtaaaaggctaagtttgatctgtattagctacctgactagattgtttc---ttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
        | |   |||| |  |  ||  | || |  | | | |  | |   | | | || ||   || ||     | || | | |||    | | | |   ||| ||||| |||||||| ||||||||||| || || |||||||||||||| || ||||||||  ||
-----gtcaagttctctatttaacattataattcaatagtagaatcatgtacactgtaatttggcataactgttgtattaaactctttgatatgcatttttacagTGCTGTGCCATCTGCGGTGTTTTCCCAACCTCCAATTGGACAAGTTGGACTCACTGAAGAGAAG

upper sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G172322_T02 (Zea mays), 3'ss of exon 6
--ccctgagaaggaagtctaatacaagtt-tgagtttaaatggtaaaaggctaagtttgatctgtattagctacctgactagattgt-ttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
     ||   |    |||  | ||  |   || |   |     |  | || ||    | | ||  | |  | ||    | |   ||  ||    || |  |||||||| |||| ||||||||||| ||||| ||||| || |||||||||||||||||||| || |||
gattgtgtctatcccgtccgacactggccatggggccatgctatttatggata----tcaactcaactgaccactcttccattgtgaattacaatttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG

upper sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G03740.2 (Glycine max), 3'ss of exon 6
ccctgagaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtttgatctgtattagctacctgactagattgtttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
  |  |  |    |  |  |||   |   || ||| |   |     | |    |   ||        | | |||| |   || | |       |    |||||||| || |||||||| ||||| || ||||| ||||||||||||||||||||||| ||||||
tgcccatgaaattggatggtactcatcgtagcttatactctgctgtgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG

upper sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G16010.1 (Glycine max), 3'ss of exon 6
---ccctgagaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtttgatctgta-ttagctacctgactagattgtttcttcttatgagc-agAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
     |  |  |    |  |  |||   |   || ||   || |    |  | |||   ||   ||     | | |||| |   || | | | ||||| | | |||||||| || |||||||| ||||| || ||||| ||||||||||||||||||||||| ||||||
acatgcccatgaaattggatggtactcatcatagcttctctgctgt--gttttagt--aattcatagcctcccaactgattctgttatat-tccttatcatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG

upper sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G54660.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------ccctga--gaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtt-tgatctgtattagctac-----ctgactagattgtttcttcttatg-----------agcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
                                                  |||  || |  ||| |    |  ||||    ||| ||| |  |    | |  | | |  | |  || ||       ||||     ||  | |||  | ||           |  |||||||| || |  || || || ||||||||||||||||||  ||||||||| |||||||| |||
gtaacataacaatcttaacttttgatgtttaaacctttgggattttttggtgattgatgagagtttttctct-gtttagtcttacatgctgcatcagtgatctataacattttataactgttgtctctgatggcttttatcctttctgtgttctataatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCTAACTGAAGAGCAG

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|37185016|gb|CF604369.1|CF604369
EST:     GCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAG                         AGCTGTACCATCCGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
genomic: GCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAGgtgttctatc ... ttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
EST: gi|110723818|gb|EE099103.1|EE099103
EST:     GCATTANCTAAAACTCTATTTGGGAATGAACCA-CAAAACCAGATTATAG                         AGCTGTACCATCCGCTGTGTTTTCCCACCC-CCTATTTGAACA-GTTGGTC
genomic: GCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAGgtgttctatc ... ttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGA-CAAGTTGGTC
EST: gi|110380596|gb|EC945872.1|EC945872
EST:     CTATTTGGGAATGAACCAACAAAACCAGATTATAG                         AGCTGTACCATCCGCTGTG-TTTCCCAGCCACCTATTGGACAAGTTGGTCT
genomic: CTATTTGGGAATGAACCAACAAAACCAGATTATAGgtgttctatc ... ttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
EST: gi|352764472|gb|FQ472829.1|FQ472829
EST:     GCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAG                         AGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
genomic: GCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAGgtgttctatc ... ttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
EST: gi|30300982|gb|CB977776.1|CB977776
EST:     AACCAGATTATAG                         AGCTGTACCATCNGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
genomic: AACCAGATTATAGgtgttctatc ... ttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
EST: gi|30300914|gb|CB977708.1|CB977708
EST:     GCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAG                         AGCTGTACCATCCGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT
genomic: GCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAGgtgttctatc ... ttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctaagtttgatctgtattagctacctgactagattgtttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
                        acctgac  putative branch site (score: 3)
                                   ttgtttcttcttat  putative PPT
              tgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctgagaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtttgatctgtattagctacctgactagattgtttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - -agaagga
- - - - - - - - -aatacaa
- - - - - - - - - - - - - - - - - - - ggtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacctg