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

...attccaagtcatgttgattttgacgtttcccctgcactcatgcttcttctcttccttcagcagctaaattaggtgctcatttgtttaaaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG

Basic information

species Vitis vinifera
transcript Vv01s0011g04210.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04210.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G25670.1 (Glycine max), 3'ss of exon 7
attccaagtcatgttgattttgacgtttcccctgcactcatgcttcttctcttccttcagcagct---aaattaggtgctcattt--gtttaaaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
  |     |  | ||  |  | |  ||||   |  | | |   ||  |||  |   | |  |  |   ||| || ||    |  |   ||  |||||| |||||||| || |||||| | || |||||| | |||||||| || || ||||| ||||| ||||| |||||||||||| |||| || |||||||||||||||||||
-gtatgtattttattactcataagctttcatttataataaccttttctctggtttgttaaaaagtggaaaactatgtctataactcaattgtaaatctattgcagTCTCTTGGAAGCATAGTAGCATTTGAGGCCATGGTGTCCATAGCAACAATTGGCCTCTATATTGCTTATGCCTTCCCTATATTCTTTAGGGTGACCTTGG

upper sequence: Vv01s0011g04210.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G41560.2 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------attccaagtcatgttgattttgacgtttcccctgcactcatgcttcttctcttccttcagcagc--taaattaggtg-ctcatttgttta-aaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
                                                                           ||      |||| |  |||||    |  ||     | | |   ||||    ||  || |  ||    ||| || ||  || | |   ||  |||||| |||||||| || |||||| | || |||||| | |||||||| || || ||||| ||||| ||||| |||||||||||| |||| || ||||| |||||||||||||
gtccctatatatgcagtttggctttctgttttcatatcattttgcatggcactgacagtatgtattttattactcataagctatcatttatattttataataacctgcaaatttagttttctctgatttgttgaaaagtggaaaactatgtttcttactcaattgtaaatctattgcagTCTCTTGGAAGCATAGTAGCATTTGAGGCCATGGTGTCCATAGCAACAATTGGCCTCTATATTGCTTATGCCTTCCCTATATTCTTAAGGGTGACCTTGG

upper sequence: Vv01s0011g04210.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G41560.1 (Glycine max), 3'ss of exon 7
------------------attccaagtcatgttgattttgacgtttcccctgcactcatgcttcttctcttccttcagcagct--aaattaggtg-ctcatttgttta-aaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
                  ||      |||| |  |||||    |  ||     | | |   ||||    ||  || |  ||    ||| || ||  || | |   ||  |||||| |||||||| || |||||| | || |||||| | |||||||| || || ||||| ||||| ||||| |||||||||||| |||| || ||||| |||||||||||||
gtatgtattttattactcataagctatcatttatattttataataacctgcaaatttagttttctctgatttgttgaaaagtggaaaactatgtttcttactcaattgtaaatctattgcagTCTCTTGGAAGCATAGTAGCATTTGAGGCCATGGTGTCCATAGCAACAATTGGCCTCTATATTGCTTATGCCTTCCCTATATTCTTAAGGGTGACCTTGG

upper sequence: Vv01s0011g04210.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G25680.1 (Glycine max), 3'ss of exon 7
------------------attccaagtcatgttgattttgacgtttcccctgcac----tcatgcttcttctcttccttcagcagctaaattaggtgctcatttgtttaaaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
                    |   | | ||  | |  |  |  |||    |  |     | ||| ||  ||    |  | | ||  | | |   |   |   |       ||| | |||||||| || |||||| | ||||||||| | || ||||| || || ||||| ||||| ||||| || ||||||||| | || || |||||||||||||||||||
gtacgtgttttattataagctttcatttataataacctgcaaatttagtttttatcattttatgtttagtcatagctcttatcattttattcttgccatgtctctaactcaatatattgcagTCTCTTGGAAGCATAGTGGCATTTGAGGCTATGGTGTCCATAGCAACGATTGGCCTCTATATAGCTTATGCCTTACCTATATTCTTTAGGGTGACCTTGG

upper sequence: Vv01s0011g04210.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S47_191V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------attccaagtcatgttgattttgacgtttcccctgca-ctcatgcttcttctcttccttcagcagctaaattaggtg-ctcatttgtttaaaatcttttg------------cagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
                                      |      |   |||    ||| | || || ||||| ||  ||    |    ||  |        |    |   || | ||||  ||      |  |||            ||||| ||||| ||||| ||||| || ||||||||||| || |||||||| ||||| || |||||  | || || || |||||| | ||  | || ||| | |
gtgagaccagactctaaaaccaccatattctctcgttgtgttgcattgcgtttgcgttg-cattgccactgcatctggtgagcttgtgattggtgtgatgtgtcgtctttctgacccattgattcggggcccgttgaaatgggggagccagTCGCTGGGGAGCCTGGTGGCGTTCCAAGCCATGGTGTCGATTGCAACAATTGGGCTGTACATCTCCTACGCGCTGCCCATCCTTTTCCGCGTCACCATAG

upper sequence: Vv01s0011g04210.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ12429 (Selaginella moellendorffii), 3'ss of exon 7
attccaagtcatgttgattttgacgtttcccctgcactcatgcttcttctcttccttcagcagctaaattaggtgctcatttgtttaaaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
                                 |     || | ||| || || ||   |  |||  | |       |||   |||  |   |||| ||||   ||||||||   || || |||||||| |||||||||||||||||||| || || |||||||| || |||||||| || || ||  | || ||| | |
---------------------------------gtgagtat-cctctactatttctc--gttgctggactcaccaa-catggtttttgatatttttccagTACTTGGGAAGCAGCGTTGCGTTTCAAGCTATGGTATCAATTGCAACTATCGGCCTTTACATTGCATACGCCCTCCCGATATTTTTCCGCGTTACCATCG

upper sequence: Vv01s0011g04210.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ34087 (Selaginella moellendorffii), 3'ss of exon 7
attccaagtcatgttgattttgacgtttcccctgcactcatgcttcttctcttccttcagcagctaaattaggtgctcatttgtttaaaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
                                 |     || | ||| || || ||   |  |||  | |           | ||| | || |||| ||||   ||||||||   || || |||||||| |||||||||||||||||||| || || |||||||| || |||||||| || || ||  | || ||| | |
---------------------------------gtgagtat-cctctactatttctc--gttgctcgactcaccaacatggtttttgatattttttccagTACTTGGGAAGCAGCGTTGCGTTTCAAGCTATGGTATCAATTGCAACTATCGGCCTTTACATTGCATACGCCCTCCCGATATTTTTCCGCGTTACCATCG

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|110696911|gb|EE073436.1|EE073436
EST:     TAAATGCAGTTTGGCTTTCTGCTGCTATATCATTTTGTATGGCATTGACG                         TCACTGGGAAGCCTTGTGGCATTTCAAGCTATGGTATCAATTGCAACTATT
genomic: TAAATGCAGTTTGGCTTTCTGCTGCTATATCATTTTGTATGGCATTGACGgtatgattct ... tcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATT
EST: gi|110732700|gb|EE108226.1|EE108226
EST:     TAAATGCAGTTTGGCTTTCTGCTGCTATATCATTTTGTATGGCATTGACG                         TCACTGGGAAGCCTTGTGGCATTTCAAGCTATGGTATCAATTGCAACTATT
genomic: TAAATGCAGTTTGGCTTTCTGCTGCTATATCATTTTGTATGGCATTGACGgtatgattct ... tcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATT
EST: gi|30130283|gb|CB915622.1|CB915622
EST:     TAAATGCAGTTTGGCTTTCTGCTGCTATATCATTTTGTATGGCATTGACG                         TCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATT
genomic: TAAATGCAGTTTGGCTTTCTGCTGCTATATCATTTTGTATGGCATTGACGgtatgattct ... tcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcttccttcagcagctaaattaggtgctcatttgtttaaaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG
                agctaaa  putative branch site (score: 3)
                                             tcttttgc  putative PPT
                                 atttgtttaaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attccaagtcatgttgattttgacgtttcccctgcactcatgcttcttctcttccttcagcagctaaattaggtgctcatttgtttaaaatcttttgcagTCACTGGGAAGCCTTGTGGCATTTCAAGCCATGGTATCAATTGCAACTATTGGACTCTACATTGCTTATGCCCTCCCCATCTTCTTTAGGGTGACCTTGG

- -ccaagtc
- - - - - - - - - - - - - ttcccct
- - - - - - - - - - - - - - - - -gcactca