Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG

Basic information

species Vitis vinifera
transcript Vv04s0023g01940.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 3'ss of exon 2
--gtgtgtat-gcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctc-ttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG
  | ||| |  |  |||      ||  | |   |||  ||       |  |  |  |  || | | |   |  |   | | | |  | |   |||| || ||  | ||||||||||||||||| ||||||||||| ||||| || ||||||||| | || ||||| ||||||||||||||  | |||
gtgagtggagagggattcctcacttgggctcaattttgtttgattcgagtggataatcgtgcttagttgttcctcccttgctgttgcgtcgcagCTTGTCGTGGTGTATGTGGATTTCAAGCTCGACGAGAGCTATACGCCTAGCAAGATCTCTGTCCGGGCCGGCGATGGCTTCCACAATCTCAAG

upper sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG-------
  |||  |||     | |   |   | |  |||    ||   | ||    ||||||||  |||| | ||||     |  || |     |||| |||||  | || |||||||||||||| |||||||| ||||||||||| |||||||| || || ||||| ||||||||||||||| | |||       
--gtgcctgcttcagtagagatgctactcctttg---ccttgtgattcgatggttttga-gactaattggttctatg--ttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT

upper sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG
  |||  |||     | |   |   | |  |||    ||   | ||    ||||||||  |||| | ||||     |  || |     |||| |||||  | || |||||||||||||| |||||||| ||||||||||| |||||||| || || ||||| ||||||||||||||| | |||
--gtgcctgcttcagtagagatgctactcctttg---ccttgtgattcgatggttttga-gactaattggttctatg--ttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG

upper sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G174971_T01 (Zea mays), 3'ss of exon 2
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG
  |||  |||     | |   |   ||| | | |||  |   | ||    ||||||||  || | |  |||   ||  || |  |   |||| ||||   | || |||||||||||||| ||||||||||||||||| || |||||||| || || ||||| ||||||||||||||| | |||
--gtgcctgcttcagtagagatgctattctct-cttggcttgtgattcgatggttttga-gattaatcggttc-tatgttgcg-tggcagCTTGTTGCTCTCTACGTGGATTTCAAGCTCGACGAGAGCTACACGCCCAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTCAAG

upper sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G25220.1 (Glycine max), 3'ss of exon 2
---------gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctctt---aaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG
          | |    |  || || |   |  ||      |  | |    |     |||| |||   |   ||||     ||  ||||| | ||     || |  ||||  | || |||||||||||||| |||||||| ||||||||||| ||  | || || || ||||| ||||| || ||||||||||||
agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatata--tgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG

upper sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G20840.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------gtgtgtatgcaatt-ttgggtttctgatttttttctttcccc---cttatcgtttggttttggtgactgaatggtgaa--tagatttctcttaa-------agCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG-------
                                                              ||    | |   || |    ||  ||  |  |||  | | |    || | | | |     || ||   |||| || |     | ||||  ||         || || ||||  ||||||||| ||||||||| |||||||| ||||||||||| ||  | || || |  ||||| ||||| || ||||||||||||       
gtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT

upper sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G06190.3 (Glycine max), 3'ss of exon 3
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG
    ||| |   || |   |   | |  |     |       |||    ||  |||| ||   |    |||           | |   || || ||||  | || |||||||||||||| || ||||| ||||||||||| ||  | || || || ||||| ||||| || ||||||||||||
----gtacg---ttgtaaataaataaaataaagttagagtttttaaatgttaatttttgtttttttggggt-----------tgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG
                                           tttctctt  CT-rich tract
                                     aatagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG