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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaaaagaacattgaaaatagtctcttctaataatgatttccatatacttctttaacagaaatacctttttttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT

Basic information

species Vitis vinifera
transcript Vv16s0022g01210.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g36250.1 (Oryza sativa), 3'ss of exon 1
tgtgaaaagaacattgaaaatagtctcttc-taataatgatttccatatacttctttaa-cagaaataccttttt-ttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
  | |  |      |    ||  | ||| | | | ||| | | | |  |||    |||| ||  | ||| ||| | || ||  ||  | ||   |   |  || ||||||||||||||||| ||| | || || || || ||||||||||| || || |||||||| || ||||||||||||||||| ||||| ||||| || 
--taagcatgcacgtatgcatgatgtctccgtgagaattactacta-gtacaaacttaatcactactacttttctattgttgatgttaattgtgtctatgcagATGGTCCAAGATTGCTGCCAAGCTACCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTCATCAAGATGGGCATC

upper sequence: Vv16s0022g01210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G037650_T01 (Zea mays), 3'ss of exon 2
-----tgtgaaaagaacattgaaaatagtctcttctaataatgatttccatatacttctttaacagaaatacctttttttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
     ||||    |  |  |  ||| |   | |   || ||  |  |  | | | |     | || ||  || || | | ||  |    | || ||    |  || |||||| |||| ||||| ||||| ||||||||||||||||| ||||| || || |||||||| || ||||||||||||||||||||||| ||||| || 
gctcatgtgcttcgttctctagaaacaaaatatcacaacaaccagctaaaaaaaat-----atcacaaccactttgtgtgctcctaatgacttgaacctgtgcagATGGTCCCAGATCGCTGCCAAGTTACCTGGAAGAACAGACAATGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTTATCAAGATGGGCATC

upper sequence: Vv16s0022g01210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G138427_T01 (Zea mays), 3'ss of exon 1
------tgtgaaaagaacattgaaaatagtctcttctaataatgatttccatatacttctttaacagaaatacctttttttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
      |       |  |||         |||| |  || ||    |||||  |||||  |  ||  |     ||    | ||  | ||    ||||       || ||||||||||| ||||| ||||| ||||| ||||||||||||||||| || || |||||||| || |||||||||||||||||  |||| ||||| || 
acctgtttctttccgctcatgtgcttcgttctcctgaaacaaaatattccaactactttatgcactcagca--ctccgatcctaatggc----ttaacctacgcagATGGTCCAAGATCGCTGCCAAGTTACCTGGGAGAACAGACAACGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTCGTCAAGATGGGCATC

upper sequence: Vv16s0022g01210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G104551_T03 (Zea mays), 3'ss of exon 1
----tgtgaaaagaacattgaaaatagtctcttcta-ataatgatttccatatacttctttaacagaaatacctttttttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
    |  |  | | ||     |  |  |  |  ||| |  || | |    | || |  ||| | |   |    || ||| || | ||||  ||    ||    || ||||| ||||||||||| ||| | || || || || ||||||||||| || || |||||||| || ||||| ||||||||||| ||||| ||||| || 
ttactcgggcatgtactccccatgtcttggcgactagacgattagtcatgt-tattaatttcatacttac-tattctttcctatatgcatgttctcctgc---agATGGTCGAAGATTGCTGCCAAGCTACCGGGCAGGACTGACAACGAGATCAAGAACCACTGGAACACGCACATTAAGAAGAAGCTGATCAAGATGGGCATC

upper sequence: Vv16s0022g01210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G12350.1 (Arabidopsis thaliana), 3'ss of exon 1
tgtgaaaagaacattgaaaatagtctcttctaataatgatttcc-----atatacttctttaacagaaatacctttttttctttttgcaattttaat-tgttt-tagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
       | | |      || |      || ||| || ||||        || || | || ||   || ||    | ||||||       |||| || | | | ||| ||||||||||| ||||| |  || || ||||||||||||||||| ||||||||||| |||||||| || ||||||||||||||  | || |||| ||| 
-------acatctccaccaacacctagctcaaatcattatttttcaaaggtaaacatattcaatgtaactaaacatatttcttaaaattctttttatgtatatatagATGGTCCAAGATCGCTGCAAGATTACCAGGAAGAACAGACAACGAAATAAAAAATCATTGGAATACTCATATCAAGAAGAAGCTCCTTAAGATGGAAATC

upper sequence: Vv16s0022g01210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G22680.1 (Arabidopsis thaliana), 3'ss of exon 1
--tgtgaaaagaacattgaaaatagtctcttctaataatgatttccatatacttctttaacagaaatacctttttttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
  | |   ||||   |   | ||| | ||  | || | |   |   ||||  ||  ||     || ||  || || | ||    | |||     | || ||||||||| ||||| ||| | |  || |||||||||||||| ||||| |||||||| || |||||||| || ||||||||||| ||| | || |||||||| 
tctataccaagattgtaacatata-tatccaccaacactttataaaatattatttattcttgtaattaatttgttat-ttaaaaccattggttgtattatagGTGGTCTAAGATAGCTTCAAGATTACCTGGAAGAACAGATAACGAAATAAAAAACCATTGGAATACTCATATCAAGAAGAAACTTCTTAAGATGGGAATC

upper sequence: Vv16s0022g01210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S433_19V6.1 (Physcomitrella patens), 3'ss of exon 2
tgtgaaaagaacattgaaaatagtctcttctaataatg-atttccatatacttctttaacagaaatacctttttttctttttgcaattttaattgt-----tttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
  | | |  | | | |   |  ||      |  |  || |   ||  | || ||    | ||| ||    |||||   | |   ||||||   |||     | ||||||||| ||||||||     || | |||||| | ||||| ||||||||||||||| |||||||||| ||| | ||||||||||||  ||  |||||  | 
attcagactagcttaggtcaacgtgggcattggttttggaaacccgaagacgtcc---aaagagatg---tttttcagtgtgataattttccgtgtccacttctagGTGGTCAAAGATTGCGATGCAGCTTCCTGGACGCACAGATAACGAGATAAAAAATTACTGGAATACGCACTTGAAGAAGAAGCTTTGCAGCATGGGCTTG

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|161715521|gb|FC067101.1|FC067101
EST:     GAGGCTGAAGAACAGCTGGTCATCGATCTCCATGCCCGCCTTGGCAATAG                         GTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAA
genomic: GAGGCTGAAGAACAGCTGGTCATCGATCTCCATGCCCGCCTTGGCAATAGgtatctacct ... attgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacttctttaacagaaatacctttttttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT
                                        ttttaat  putative branch site (score: 3)
                                              ttgtttt  CT-rich tract
                       tttttttctttttgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaaaagaacattgaaaatagtctcttctaataatgatttccatatacttctttaacagaaatacctttttttctttttgcaattttaattgttttagGTGGTCCAAGATTGCTGCTAAGTTGCCTGGAAGAACAGACAACGAGATAAAAAATCACTGGAATACCCACATCAAGAAGAAGCTTATCAAAATGGGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - aaaagaa
- - - - - - - -gaaaata
- - - - - - - - - - - -tctcttc
- - - - - - - - - - - - - - - - - - - - - ccatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aacagaa