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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataaaaataaatgtttgaccattggccgatcttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC

Basic information

species Vitis vinifera
transcript Vv19s0090g00840.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G43260.1 (Glycine max), 3'ss of exon 2
-tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataaaaataaatgtttgaccattggccgatcttaatccact-at-acagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
 |||  ||   ||  || | | ||||    ||  ||  ||| |  |   | ||  || |  |   |  | ||   |       | || ||| | | || |||||| || |||||||| |||||||||||||||||||| |||||||| ||||| || ||||| || ||| |||||||||| ||| | ||||  ||||||||||
ttttgtatgtgaagttgcattctttg--agttaaaaatttctggtcgatatatcttatacctgc-tactagatattaattttcttttcatcaattcatgacagATATCAGATGGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC

upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G46280.1 (Glycine max), 3'ss of exon 4
tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataaaaataaat----gtttgaccattggccgatcttaatccactata-cagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
          ||| |    ||  || || ||| | |  | | |        | || |||| | ||    || | |   ||    |   | |||  | |||| |||||  | |||||||||||||||||||||||||| || |||||||||||||| || || || ||  |||| |||||||| ||||| |||   |||| |||||
----ggatgtaatttacg-tgggtgaagtttgcacgcattaatttcttgtttcatgaaaacacatttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC

upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G09400.1 (Glycine max), 3'ss of exon 1
tttcaatcacaatctggactg--tttgtagattggaagattcagtactccaaattataaaaataaatgtttgaccattggccgatcttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
    | | | | | ||       | |   |||   | |         |     |   ||   ||    ||||     |    | | ||  |  |   | |||||   |||||| || |||||||||||||| ||||||||||  |||||||| ||||| || |||||||| || || || |||| ||||| |||||| || |
acctattaatattttgagtcacctcttctgataaaaggggatgtgcatttgggtggaaatggtatgattttgcattataattgctatt--ttaatgtttcagATGGGCGATGGGTGTCAATGGAGAAAGTACGGACAAAAGACAGCGAAAGGCAACCCTTGTCCTCGAGCCTACTACCGTTGCAGCATGGGAACTGCATGCC

upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G20990.1 (Glycine max), 3'ss of exon 4
tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataa--aaataaatgtttgaccattggccgatcttaatccactata-cagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
   |||| | | |   | |   |  |    |  |||      | |     | || ||  ||   ||||  |   |||| |    | ||| |  | | |  ||||| |  ||||| || |||||||||||||| ||||||||||  |||||||| ||||| || |||||||| || || || || | ||||| |||||| ||||
---caattaaagttgagtcacctcttctgataaaagggaatttgcatttgactaaaattaatggaatgaatatgcatttgtaattgttattttaatctttcagATGTTTGATGGGTGTCAATGGAGAAAGTACGGACAAAAGACAGCGAAAGGCAACCCTTGTCCTCGAGCCTACTACCGTTGTAGCATGGGAACTGCATGTC

upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G04710.1 (Glycine max), 3'ss of exon 4
tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataaaaataaatgtttgaccattggccg--atcttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
| |  ||    || |  |    | ||| | |   | |     ||    | |||  | |||   || |  ||  ||     |  ||||||||  | | | |||||    ||||| |||||||||||||| ||||||||||||||  | || || || || |||||||| || || ||||| |||| ||||| ||| |||||||
tatatatatatatatatatatctagtatactaataaaaatgatatatgacattgaagaaaactatttacgataatgcattggcatcttaatt-attct-cagATGGGTGATGGGTGCCAATGGAGAAAATATGGACAAAAGATATCAAAGGGCAATCCTTGCCCTCGGGCCTACTATCGCTGCAACATGGGAACAGCTTGTC

upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G17800.1 (Glycine max), 3'ss of exon 5
tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaatt---ataaaaataaatgtttgaccattggccgat-cttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
  |  ||    || |  | | |||||  |||| |  | | |  |    | |||   ||  ||  |||   || || ||    |  | | | ||  | | | |||||    ||||| || ||||||||||| ||||||||||||||  | || || || || || ||||| || |||||||| |||| ||||| |||||| ||||
--tatatatatatatata-tatttgtgcattgcactaataaaaatgaaatattgacattgaagaaaactatttacgataatgcattgccttatatatttt-cagATGGGTGATGGGTGTCAATGGAGAAAATATGGACAAAAGATATCAAAGGGCAATCCTTGTCCTCGGGCCTATTATCGCTGCAACATGGGAACTGCATGTC

upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
tttcaatcacaatctggactgtttgtagattggaagattcagtactc--caaattataaaaataaatgtttgaccattggccgatcttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
  | | |     | |    |  |  ||  ||  |||| |   ||      ||| |||     | |  | || |  ||      |  |||     |||||  |||   ||||||||| ||||||||||| ||||| || |||||||| ||||| || || || || || || ||||| || ||||| ||||| || |  ||||
-gtaagttgatttattagatactaatac-ttataagactatataaaaaataaactatgtgctttagagattaattatctttgtactttatgtttctata--gATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC

upper sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S47_251V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------tttca----atcacaatctggactgtttgtagattgga----agattcagtactccaaattataaaaataaatgtttgaccattggccgatcttaatccactatac-----agATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
               |||||    | |    |||  ||  |||  | |||        |||||||| ||    ||  | ||  |  |     | ||  ||  |   | | ||    |||       |||||   || |||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||| || || || ||||||||| | ||  | |  ||||
gtacgttcctgtccttttcatagaacccttctctacacgcttttaaaattcagcaccggattcagtgcttttcatcgttaaggtttaatcgggtcccatgatctcacatgatgatttatctgttttagATCAATGACGGATGCCAGTGGAGGAAATATGGTCAGAAGATGGCGAAAGGGAACCCCTGTCCTCGTGCATACTACCGATGCACCGTTGCGCCGGGCTGTC

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|161711693|gb|FC059960.1|FC059960
EST:     TGATGAGGAAAGCTCGGGTTTCAGTTCGAGCAAGATCGGAGGCATCTATG                         ATCTCCGATGGAT
genomic: TGATGAGGAAAGCTCGGGTCTCAGTTCGAGCAAGATCGGAGGCATCCATGgtaagtaaac ... cactatacagATCTCCGATGGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaaattataaaaataaatgtttgaccattggccgatcttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
                                     tcttaat  putative branch site (score: 3)
     attataaaaataaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataaaaataaatgtttgaccattggccgatcttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - -cacaatc
- - - - - - - - - ctgtttg
- - - - - - - - - - - - - - - - - - - - - - ctccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattgg