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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaagatactgtatattatttggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT

Basic information

species Vitis vinifera
transcript Vv08s0007g00120.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g38550.2 (Oryza sativa), 3'ss of exon 4
gaaaaagatactgtatattatttg---gcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT
  ||   ||  || |   |    |    | ||      | | ||| ||     | | |  | ||  ||| |  ||   |||| |  |    | | || ||||||||||||| |||||| |||| ||||| || ||||| || |||||||||||||| ||||| |||||||||||||| |||
--aattcattttggaggcttggcgcgcacttatcagtgttaatttggaagatttgtggtcaattattttcttgctaa-attattttgtgcttgtaacttgcagGTTGAAAGTATAGTTCTGAGCATCATTTCGATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAATATTGAAGCGGCT

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
gaaaaagatactgtatattatttggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT
 |     ||  | | ||   ||| | |    | |||   ||    |    |  |  ||||     ||    |  | ||| || |    || ||  | |||||||| ||||||||| |||| ||||| || ||||||||  |||||||||||||||| || |||||||||||||| |||
tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
----gaaaaagatactg-tatattatttggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT
    ||   |    ||| |  ||||  |    |  |  ||||| |    | |      || |   || |  || | ||   || ||| | |  |||   |||||||||||||| |||||| |||| ||||| |||||||| || ||||| ||||| || ||||| ||||||||||||||||| 
tgttgatgtatgccctggtccattaact--tctgtttgcatcagtagaaactaatcaatg-tgcatgttgctttagttaatttgctgtgct--ttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
gaaaaagatactgtatattatttggcatactgaca----tcacttttgattcccttttggtatttgctttt--tgacttttattactgggatggtttcacat--gcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT
          ||   |   | | || | |  || |    ||  | |||| |      || | | || | |   |   | |||       ||| |||   |||  |||||| |||||||||||| |||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||| || |||
--------gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 4
-gaaaaagatactgtatattatttggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggt--ttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT
   | |  || || | | ||  |  |  ||||    |||  | ||| | | |||  ||||    |   |   | |||        || ||  | ||  |||||||||||||||||||| |||| || ||||||||||| || ||||||||||| || ||| | ||||| ||||| || |||
gatacagaatgctttgttttggtcag-gtacttctttcatgtgtgagtactttt--gtatgctatcactagttgttaagttgattattgttatccatttgcagGTTGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGACGAGTCTGCAGCAAACATTGAGGCAGCT

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 4
-gaaaaagatactgtatattatt-tggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT
    |   ||||| ||    ||| |    |  | |||||| | |  | |      || |   || | |||  |     |||    | |  |   | |||||||||||||| |||||| |||| ||||| || ||||| || ||||||||||| || ||||| || ||||| |||||||| 
ttttatgtatactctagcccattattttttgtttacatcagtataaactagacaatg-tgcatgttgttttccccaacttatcctgctt-tcgtaaatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCGATGCTCTCTAGTCCAAATGACGAGTCTCCAGCGAATATCGAAGCTGCC

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|37190149|gb|CF609498.1|CF609498
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|71855236|gb|DT004291.1|DT004291
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110406248|gb|EC971815.1|EC971815
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110411536|gb|EC977255.1|EC977255
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110408770|gb|EC974411.1|EC974411
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|71855279|gb|DT004334.1|DT004334
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110404984|gb|EC970511.1|EC970511
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110375077|gb|EC940034.1|EC940034
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|37183655|gb|CF603009.1|CF603009
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110409487|gb|EC975150.1|EC975150
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110398671|gb|EC965142.1|EC965142
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
EST: gi|110411501|gb|EC977218.1|EC977218
EST:     ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACG                         GTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT
genomic: ACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACACGgtacatacaa ... tcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT
                   ttttgac  putative branch site (score: 3)
                  tttttgacttttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaagatactgtatattatttggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-aaaaaga
- - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - -catcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggatgg