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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgattctaaccttcttaatatagaatactatcttaattagtagcttctgatgaaagaaatttgaaatctgtaaacattttatattttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC

Basic information

species Vitis vinifera
transcript Vv10s0116g00830.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os07g33670.1 (Oryza sativa), 3'ss of exon 13
---------------------ttctgattctaaccttcttaatatagaatactatcttaa-----ttagtagcttctgatgaaagaaatttgaaatctgtaaacattttatatt-ttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC
                     | |  |    | |      |  ||||  |||| | | |       |||||  |  | |  || | | ||||| ||    | |      || || ||  | |  |||||||||| ||||||| |||||| || ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| ||||| ||||  || | 
gtaatttgagttccaaggaaatccacagaacagcaactcgatcatagtgtactgtttaatgagttctagtacatatttaccaatgcactttgatattgaaagaatgggaatcttgttactgtggcagTTGATGAGCGGTGTGGTATGGAACTAGATGAGACTGATCCTGCTGTCTGGCTTAAGTTGGAAGCTGCAACTGATGAGTACATTCAGAAAAACTTTCAAGA

upper sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G426556_T01 (Zea mays), 3'ss of exon 11
--------------------------------------------------------ttctgattc-taaccttcttaatatagaatactatct----taattagtagcttctgatgaaagaaatttgaaatctgtaaacattttatattttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC
                                                         |  |||   || | |  | |  |||   |  | |         ||  ||  ||   |   ||  ||  || |   |  ||  | |  |   |   | ||  |||| ||||||||||||| ||||||| | ||||| ||||||||| |  ||||||| || ||||||||||||||||| |||||||| ||||| ||||  | | |
gtaaatcaactcaaaggaaactcttagcatttgctagaagagaaactattaatgtgctgggatctgtagcatcataaccataatttgttgtgcactacttttgatatgtttcaacctaattaacctgcatattcaaatgagtgaactctcaatgttggcagTGGATGAACGGTGTGGTATGGAGTTAGATGAAACTGATCCTACTATCTGGCTGAAGTTGGAAGCTGCAACTGATGAGTACATTCAGAAGAACTTTCTGTC

upper sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 7
---------------------------------------------------------ttctg-attctaaccttcttaatatagaatactatct----taattagtagcttctgatgaaagaaatttgaaatct---gtaaacattttatattttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC
                                                         || ||   | || |      |  |||   |  | | |       ||  ||  ||   |   || ||   ||     |    ||||         |  |  |||  |||| |||||||| |||| ||||||  | ||||| |||||||||||  ||||||| || ||||||||||||||||| |||||||| ||||| || |  | |||
gtaattcaacttcaaaggaatcccttaaaatttgctagaagagaaactattaacttgttgtgcgctgtagcaacacaaccataatttgttgtgtactacttttgatatgtttcaacctaataagcctgtgtattcaaataaatgagcctcttcctactttggcagTGGATGAACGATGTGGTATGGAATTAGATGAAACTGATCCTGCTATCTGGCTTAAGTTGGAAGCTGCAACTGATGAGTACATTCAGAAGAATTTTCTGGC

upper sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 12
ttctgattctaaccttcttaatatagaa---tactatcttaattagtagcttctgatgaaagaaatttgaaatctg--taaacattttatat-tttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC
     ||| |  |||  || ||| ||||   ||||     | |   |||||  | ||| ||  || || || ||||   ||   || | | | | | |  | |||||||||||||| ||||||||||| || |||||||| |||||  |  |||||||||| |||||| |||| | ||| || || || || || ||    || ||
-----attttc-cctgtttgataaagaagtgtacttctagagtagctagctattcatggaaagaactttaattctgaacaagtgttctttgtgtctttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC

upper sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA17G01850.1 (Glycine max), 3'ss of exon 13
ttctgattctaaccttcttaatatagaa---tactatcttaattagtagcttctgatgaaagaaatttgaaatct--gtaaacattttatat-tttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC
       | |  |||  || ||| ||||   ||||  |  | |   |||||  | ||| ||  || || || |||    ||   |  | | | | | |  | |||||||||||||| ||||||||||| || |||||||| |||||  |   ||||||||| |||||| |||| | ||| || || || || || ||    || ||
------cttttccctgtttgataaagaagtgtacttccagagtagctagctattcatggaaagaactttaattctcaacaagtgtcctctgtgtctttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCAACTAACTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC

upper sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 13
---------------------------------------ttctgattctaaccttcttaatatagaatactatcttaattagtagcttc-tgatgaaagaaatttga-----aatctg--taaacattttatattttctttta-acagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC
                                       | ||| |    ||||    ||  | ||||    | |  ||    |  | | | ||| | |   |||||     |||||   ||| | ||  |||| |   | ||  ||||||| || || ||||  |||||| |||||||||||||||| ||  |||||||||||||||||||||| | ||| || | ||| || | |||  |||| | 
gtaacaaacagcattttacaacatgcaagaacactcttatcctgttgaacacctatgaaaccttgaatttcttatccatgccgatttccataatgcatgtgttttgacgtagaatctagttaatctttacatatctgggtatatgcagTTGACGATCGCTGTGGAATGGAGTTGGATGAGACTGATCCAGCGATCTGGCTAAAATTGGAAGCTGCGATTGAAGAATTCATACAAAGCAATCCCCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttctgatgaaagaaatttgaaatctgtaaacattttatattttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC
  ttctgat  putative branch site (score: 3)
                                  ttttatattttctttt  putative PPT
              aaatttgaaatctgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgattctaaccttcttaatatagaatactatcttaattagtagcttctgatgaaagaaatttgaaatctgtaaacattttatattttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- ctgattc
- - - - - - ccttctt
- - - - - - - - - - - - agaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaca