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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------gtatctttattttgcaatgtc--taatatct---tgttc-tgaaatgaattctgaagtttggggtttaatgaattattgaatattaatt-tatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
                                      ||||  |  |  |  ||  |   || |||||   ||||  | ||  ||||| |      ||   |||||   |   |||| |  ||    |   ||    ||| |  |||||||||||| || ||||| ||  | || || || ||||||||||| ||||| || ||||| ||||| || |||||  | ||||| ||||||||||||||
gtattactcctttgtactgatttctcttaaagttatgtgtattctcttgctaaaactttagtattatctatttgtttgtaaagagaattttaccaagtgccatttaacttaaacttgagtgataccaattccttgaaatttttgcagCTTTTGTGGAAAAGATGCAGACTGGGGGTGACCTCAATCTCATTGGGCAATTCGGTGTTGGTTTCTATTCAGTATACTTGGTTGCTGACTATGTTGAAGT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
-----gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaat--attaatttatattttct----tttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
     |  | || || || | |   || || |  ||  || | |  | || |  | |||    |   |   |||||    |  | ||||||  | | | |    ||| |  |||||||||||| || |||||  |  | || || || ||||| |||||||| ||||| ||||| ||||||||||| ||  | ||||| ||||||||||||||
gtactgccttttcatctttccag--ctgat-tactgcactcacaatatttgttta-tttataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 5
gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttctttta-tatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
|||  | | || || |      | |||    | ||||| | | || ||    ||| | | |  |     ||   || ||||||     | | | ||| |  ||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||| || |||||||| || ||||||||||| |||||||| || |||||||| |||||
gtacgtatgttgtgga-----cattat----tgctgaagtaatttttg---cttgtgatgtggttgggaat---atgttaattggagctgtgtgttaattcagCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTTGTGGCCGACTATGTCGAAGT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5
gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
          | || |   | |   |  |||  ||||| |   || ||    |||   | |  |     |    || ||||||     | | ||  ||  ||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||| || |||||||| || ||||||||||| ||||| || || |||||||| |||| 
--------ggtatgtatgttgtggcacattg--ctgaagtagtttttg---cttgtaatgtggttgggaa---gatgttaattggagctgtgtta-attcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
|||  ||  || ||   ||    |||  |||| ||| |   |||     ||| |||   | ||| ||||     |||||   | | || ||   ||    ||||||||| |||||||||||| | ||||||||| | || || |||||||||||||||||||| ||||||||||  ||||||||||| |||||  |||||||
gtacgttacttatgtggtg----atacgttgtcctgcat--aat-----agtatgga--tcaataaattcc---atattt-ctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
                                                                                            | | ||    ||  || ||| ||  | |    || | | |  ||    || |        |  |  |||| ||||      | | | || | |    | |||||||  ||||| | |||||||   | |||||||| || ||||| || |||||||||||||| ||||||||||| ||| | ||||| ||  | ||||||||
gttagcgagctggtctgcatgcgacagtaatatattaggaaacatatcctacaaaattctgtcacagttactggtatatgaatacttggaatgaaactcaccttctcagtgtataggagcactatccgga-tacatatgtaactcgatcaagtctttcattaatgaaggaatgtctgtcttgtgtgcggtgtagCTTTCTTGGAGCAGATGCAAAAAGGAGGGGATCTCAACCTCATAGGTCAATTTGGAGTTGGTTTCTACTCTGTGTATTTGGTTGCTGATCACGTTGAAGT

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|110723753|gb|EE101423.1|EE101423
EST:     GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAG                         CTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
genomic: GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttat ... ttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
EST: gi|30297571|gb|CB974365.1|CB974365
EST:     GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAG                         CTTTTGTGGAGAAAATGCAAACCAGTGGGGATCCTAATCTCATTGGACAAT
genomic: GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttat ... ttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
EST: gi|110710305|gb|EE086522.1|EE086522
EST:     GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAG                         CTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
genomic: GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttat ... ttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
EST: gi|110709700|gb|EE085391.1|EE085391
EST:     GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAG                         CTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
genomic: GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttat ... ttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
EST: gi|110726118|gb|EE101621.1|EE101621
EST:     GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAG                         CTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
genomic: GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttat ... ttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAAT
EST: gi|110724805|gb|EE100952.1|EE100952
EST:     GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAG                         CTTTTGTGGAGAAA-TGGCAA-CCAGTGGGGATCTTAATCTCATTGGACAA
genomic: GGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttat ... ttttatatagCTTTTGTGGAGAAAATG-CAAACCAGTGGGGATCTTAATCTCATTGGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
                            tattaat  putative branch site (score: 2)
                                  tttatattttctttt  CT-rich tract
           tttaatgaattattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG