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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT

Basic information

species Vitis vinifera
transcript Vv07s0005g03730.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
---aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
   ||  ||   ||  ||  |     ||||| | |    || | |  |     || ||||   |  |         |     || |  | |   | | ||||| ||||| || || || ||||| ||||| ||||||||||| || |||||| ||||||||||||||||||| |||||||| |||||||| || |||||||||
acgaattacttggattcaagttatattatttatgtgcgaatcaaacaag---attttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT

upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
--aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
  |        | |     | ||| | ||   | | || ||    ||     |||  | ||   |    || ||  |       ||||   |     ||||| || || || ||||||||||| ||||| || |||||||| ||||||||||||||  |||| || ||||| |||||||| || || |||||||||| ||||
ccatttgttttgtgtggattacatttgttcactgttttctttatatagtc--ttaactgtgtataacgtttactgagttaataatcttggatcatggtgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT

upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
-aacaa-cagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttc----acttcaa--ctgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
 | ||| | |||   |   |||   |     |         ||   | | |   |                 |    || |  | || |     | |||   |  || || ||| || || || |||||||| || || ||||||||||||||||||||||||   || || || |||  | | |||||     | ||          
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------

upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
aacaacagagagaca-catgcata-tatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaac-tgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
   | |||   | |  || | | | || || |  ||  |  |  | | ||     ||| |||| |||      |||||   || |  | |   |  | ||||| ||||| || |||||||| || ||||| ||||| ||||||||||||||||||||  ||||||| ||||| || || ||||||||  ||||| |  |||||
--tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaa-gtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT

upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
aacaacagagagacacatgcatatatttgttttat-tattagattaactagttatttatgatgatgaattgctaggccc---catgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
   |   |   | |      | |     || |  |  |||    | | |     ||| |  |  || ||   ||||| |   || ||  || ||||   ||||||||||| || |||||||| || ||||| ||||| ||||| ||||||||||||||  ||||||| || || ||||| ||||||||  | ||  |  |||||
--tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcg--tgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT

upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatga--attg---ctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
  | |  ||      | || || | |||||  ||||   || |||    | ||   | ||  || |  ||||    | ||   |||||  |   | | || |||| || ||||| |||||||| ||||||||||| ||||||||||| |||||| ||||| | ||||| || ||  |||||||||| ||  | ||  |  |||| 
-gcgagggatgagagcttggatctttttgtcatatt-ccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtg--tgcgac-gcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC

upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 7
aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
                                                |||  | |  || ||| |     || |     ||    || |   |    || || ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| || || || ||||| || |||||     | ||  | ||||| 
---------------------------------------------gtaagtcctattcga-gat-atccaatatgtttt-tgctgacagtgggatactagATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC

upper sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 7
aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
                                                 || | |  |  |   ||     || |     ||    || |   |    || || ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| || || || ||||| || |||||     | ||  | ||||| 
-------------------------------------------------gtaagtcctattcgagatacaatatgtttt-tgctgacagtgggatgctagATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
 gattaac  putative branch site (score: 2)
                                     tcttcacttc  putative PPT
     ttatttatgatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
aacaaca
- - - - - - -cacatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcccca