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

gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT

Basic information

species Vitis vinifera
transcript Vv07s0005g00740.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g21070.1 (Oryza sativa), 3'ss of exon 1
------------------------------gtatgt-gtaaatgtgtatgctctgtttct-tcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
                                || | ||     |    ||  | | ||| ||  |  ||   | |   | | ||    | |     |||| |  |   ||   ||||     | |     |||||||| ||||| ||||||||||| ||||| || |||||  ||||||| ||||||||  |||| |||| ||  || |||||  | ||||| ||| | ||||
gcaagaaactctccgctcctccgcgtttcaccatttcgtcggcattggcgccgtctctctctctctctctctctctctctctctctctctctcgccatggtctcatggcttgatgcgt-----ttgtctctcagGTGGACTTGGTGGGAGGGTACTACGACGCCGGCGACAACATGAAGTTCGGGTTCCCGCTGGCGTTCAGCATGACGATGCTGGCGTGGAGCGTGGTGGAGT

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G37420.1 (Glycine max), 3'ss of exon 1
gtatg----tgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttga--agttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
|||||    | |||   | |     |    |  | | |  |  || | || ||||   |  | ||    ||     | | | ||||  || | |||     ||||||||| ||||||||||||||||||||||| || ||||||||||| |||||||| || || |||||||||||||||||||||||||| |||||||| || ||||
gtatgataatataataatattaatacaacattcttagtctca-gtctcagtttttgtgttctctggcttgtgcacatggcttatttctgcattgaatgtacaatgcagGTTGATTTGGTTGGAGGGTACTATGATGCTGGGGACAATGTCAAGTTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCGTGGAGTGTTATTGAGT

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 1
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
          |||| ||| |   ||| |      |     |   |   | ||  | ||||    || | |||| | ||||  | ||| |  || || ||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| || || ||||| |||||||||||||||||||||||||| || || ||||
--------gtatgtatataccaagttaccaactctcacattaccatgctatttgtgtttt----tttggtttgcttatttatgtgtgaatgtgcaa-tgcagGTTGATTTGGTTGGAGGGTACTATGATGCTGGGGACAATGTGAAATTTGGTTTTCCCATGGCATTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
           | || ||   |    |||   |||||       |  ||||     |||||   ||||||| | | ||||  | ||| |  || || ||||||| ||||| ||||||||||||||||| || ||||||||||| || ||||| || || |||||||||||||||||||||||||||||||| || || ||||
----------gtatgcatataccaactctcacattacc------atgttttctggtttttgtttttggttt-gcttatttatgtgtgaatgtgcaa-tgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G40030.1 (Glycine max), 3'ss of exon 2
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
                                                                                                               |||||||||||||| || |  ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||            
---------------------------------------------------------------------------------------------------------------gttggagggtactacgatgttggggacaatgtcaagTTTGGGTTTCCCATGGCCTTCACCACCACCATGCTTTCGTGGA------------

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G02290.1 (Arabidopsis thaliana), 3'ss of exon 1
-----gtatgtgtaaatgt----gtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
      | ||| | ||| |      | | ||   |  ||  |||| |||||||   |||  | |||||  ||      | |   |||||| | ||     ||       |||||||||||||||||||||||||||| ||||| |||||| | || ||||| ||||||||||| ||||| ||||| ||||||||||||||||| || || |
ttaaattctgtatcaatatcgtcaaaagatcaaatcttt--attagttgttttc--tttcccctctttccaaaaaatctct---aatttgtgtgttttgttgat----tagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
-gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
    |   |   |   |||||| | |   || ||  |       ||  ||    || || |       |  |  ||  | ||    | |   |     || ||||||||||||| ||||| ||||| || |||||||||||| |||||||||| ||||||||||| ||||| ||||| ||||| ||||||||| | || ||||
accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaa-agcctaatttgtgtgaa--ttggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttg-ttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
                                  | | | | | ||||  | |   ||||| |    | | |  || || |     |||   |     |  |||||| | |    ||||| |||   ||| | || ||||| || |||||||| ||||| ||||| ||||| | |||||||||||||||||| ||||| || |
-------------------------------gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatctc--tttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttg-ttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
                                  | | | | | ||||  | |   ||||  |    | | |  || || |     |||   |     |  |||||| | |    ||||| |||   ||| | || ||||| || |||||||| ||||| ||||| ||||| | |||||||||||||||||| ||||| || |
-------------------------------gtatgcgtttctgagatcctgctcgttttataagaagctctacttgatctc--tttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT

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|349828703|gb|FQ418438.1|FQ418438
EST:     GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCAT                         GTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG
genomic: GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCATgtatgtgtaa ... ggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG
EST: gi|351029054|gb|FQ435254.1|FQ435254
EST:     GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCAT                         GTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG
genomic: GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCATgtatgtgtaa ... ggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG
EST: gi|110700767|gb|EE077711.1|EE077711
EST:     GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCAT                         GTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG
genomic: GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCATgtatgtgtaa ... ggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG
EST: gi|351043975|gb|FQ431406.1|FQ431406
EST:     GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCAT                         GTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG
genomic: GAATGACTTGGAGGAGAGACTCTGGCCTGTCAGATGGGGCAGCCATGCATgtatgtgtaa ... ggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
                        tgttaat  putative branch site (score: 3)
                     ttttgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA