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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgttggtgctagaaatgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG

Basic information

species Vitis vinifera
transcript Vv16s0098g01040.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
--------------------acatgttggtgctagaa----atgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaat---gttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
                     |||||   |||   ||    ||   ||   ||||      ||    | |  ||        ||   ||  ||  |   |  |        || | ||  | | ||||| || ||||| ||||| ||||| || |||||||||||||| ||||| ||||| ||||||
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
acatgttggtgcta-gaaatgggtatagc--ttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaa-------tgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
  |||       |  | ||  |  ||     |   ||       | ||||   |  |   |||| |  | || |   |||  ||        | ||   |||   | |||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G069102_T03 (Zea mays), 3'ss of exon 4
acatgttggtgctagaaatgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaa-------tgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
      |   |  |   |   |  |  ||||    | || |  ||||   |  |   |||| |  | || |   |||  ||        | ||   |||   | |||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||
-----cttccggaaccgacatgcttgtcttaagttcatggc--tcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
acatgttggtgctagaaatgggtatagcttagaaacgtgc-cgatcaaacattgtttactatttct--tgtgcttgttaattaaat-----gttatcgtgtcatc--cagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG----------------------------------------
  |||        || |||    |||  |  |  | || |     | ||  ||  ||  | | |||  | || |  ||||  || |      || |  ||| |||  |||||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||                                        
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G454261_T01 (Zea mays), 3'ss of exon 1
acatgttggtgctagaa-atgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
||||  |  |||||     |   |   | ||  ||  | |    | |     ||||  | ||      |      ||     || || | |||   | |||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||
acatactattgctaccctgtttctgctgtttcaaactgagatactaaggttgtgttgccaatcctacataacatatatacttattttct-gtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G161649_T01 (Zea mays), 3'ss of exon 3
acatgttggtgctagaaatgggtatagcttaga--aacgtgccgatcaaacattgtttactatttct--tgtgcttgttaa------ttaaatgttatcgtgtcatc--cagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
  |||        || |||    |||  ||     ||  |   |    ||  ||  |   | |||||  | ||||  ||||      ||     || |  ||| |||  |||||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||
gtatgcaaccttcaggaatcaacatactttgttttaagttcatggctcaaggttcatgcttgtttctggtatgctctttaaaaagagtttggcatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G036634_T01 (Zea mays), 3'ss of exon 14
acatgttggtgctagaaatgggtatagcttag--aaacgtgccgatcaaacattgtttactatttct--tgtgcttgttaattaaa------tgttatcgtgtcatc--cagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
  |||        || |||    |||  ||     ||  |   |    ||  ||  |   | |||||  | ||||  ||||  |||        || |  ||| |||  |||||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||
gtatgcaaccttcaggaatcaacatactttgttttaagttcatggctcaaggttcatgcttgtttctggtatgctctttaaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 6
acatgttggt--gctaga---aatgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatg-------ttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
  |||    |   |||||   ||   | ||  ||||    | || |  ||||   |  |   |||| |  | || |   |||  || |        ||   |||   |||||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| |||| |
gtatgcaaatcttctagaaccaacatgcatgtcttaagttcatggc--tcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctccagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGATG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 4
acatgttggtgctagaaatgggtatagcttag--aaacgtgccgatcaaacattgtttactatttct--tgtgcttgttaattaaatgt-------tatcgtgtcatc--cagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
  |||        || |||    |||  ||     ||  |   |    ||  ||  |   | |||||  | ||||  ||||  ||| ||       | |  ||| |||  |||||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||
gtatgcaaccttcaggaatcaacatactttgttttaagttcatggctcaaggttcatgcttgtttctggtatgctctttaaaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 4
acatgttggtgctagaaatgggtatagcttagaaacgtgc-cgatcaaacattgtttactatttct--tgtgcttgttaattaaat-----gttatcgtgtcatc--cagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
  |||        || |||    |||  |  |  | || |     | ||  ||  ||  | | |||  | || |  ||||  || |      || |  ||| |||  |||||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G457231_T01 (Zea mays), 3'ss of exon 7
acatgttgg--tgctaga---aatgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatg-------ttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG---------------------------------
  |||      | | |||   ||   |  |  ||||    | || |  ||||   |  |   ||||||  | || |   |||  ||||        ||   |||   | |||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||                                 
gtatgcaaaccttccagaaccaacatgcttgtcttaagttcatggc--tcaatgttcatgctctatttgatatggtctctaagaaaattggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
acatgttggtgctagaaatgggt--atagcttagaaacgtgccgatcaaacattgtttactat--ttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
      || ||   | |||   |  ||| |  |  |   | | | |     | | | |  |||  |   |  |   |||  |  | | |    |||   |  ||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||
--tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgatatggtctctaagaaagttggtcgattttc--tgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G044246_T01 (Zea mays), 3'ss of exon 1
--------acatgttggtgctagaaa--tgggtatagcttagaaacgtgccgatcaaacattgtttactat--ttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG---------------------------------
        || |   ||  | |  |   | |   ||  ||     |     | |||  |  | | |  |||  |   |  |   |||  |  | | |    |||   | |||||||| ||||||||||||||||| || |||||||| ||||| ||||| || || ||||||                                 
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttc--tgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
--------acatgttggtgctagaaa--tgggtatagcttagaaacgtgccgatcaaacattgtttactat--ttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
        || |   ||  | |  |   | |   ||  ||     |     | |||  |  | | |  |||  |   |  |   |||  |  | | |    |||   | |||||||| ||||||||||||||||| || |||||||| ||||| ||||| || || ||||||
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttc--tgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
acatgttgg--tgctagaaatgg-gtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatg-------ttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
  |||      | |  ||| |    |     |   ||       | ||||   |  |   |||| |  | || |   |||  || |        ||   |||   | |||||||| ||||||||||||||||| || || ||||| ||||| ||||| ||||| ||||||
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G376619_T01 (Zea mays), 3'ss of exon 6
acatgttggtgctagaaatgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
                                                             |   |  |   |||     | | |    |||   |  ||||||| ||||||||||||||||| || |||||||| ||||  ||||| ||||| ||||||
------------------------------------------------------------gtatctaagaaagttggccgattttc--tgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTACACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 3
--------acatgttggtgctagaaa--tgggtatagcttagaaacgtgccgatcaaacattgtttactat--ttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
        || |  |||  | |  |   | |   ||  ||     |     | |||  |  | | |  |||  |   |  |   |||  |  | | |    |||   ||||| |||| ||||||||||||||||| || ||||| || ||||| ||||| ||||| ||||||
gtatgcaaaccttctggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttc--tgtgctctccagCCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
---acatgttggtgctagaaatgggtatagcttagaaac-gtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
   |    ||  | || | || |  | |   | | |  |  |     |  || |  | |    ||   || ||  | | | |||   ||||   |    | |||||||||||||| ||||||||||| ||  |||| || ||||||||||||||||| ||||||
ggaattgtttcatacttgcaacgattgttagtgatatgccatagttcttgaatacggctcgg-atgaattctggctctaactta---gttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 3'ss of exon 6
--acatgttggtgc-tagaaatgggtatagcttagaaacgtgccgatc-aaacattgtttactatttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
    || ||| |   |    |  |   ||| ||  |   |  |    |   | |||| || | ||    ||    |  |||   ||  |     |||  | ||||||||||| || ||||||||||| ||  | || || ||||||||||||||||||||||||
aagaattttgataaatttttagtgacgtag-ttgtatgtgaacaatcctggaaattgctt-caataaggtggttgttctaacacaacttctctatgt--ttcagTCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAG

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|110394549|gb|EC959681.1|EC959681
EST:     TACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGG                         TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT
genomic: TACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGGgtgagagtat ... tgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT
EST: gi|254917332|gb|GR906158.1|GR906158
EST:     ACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGG                         TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT
genomic: ACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGGgtgagagtat ... tgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT
EST: gi|110406292|gb|EC971861.1|EC971861
EST:     TACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGG                         TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT
genomic: TACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGGgtgagagtat ... tgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT
EST: gi|110385680|gb|EC950225.1|EC950225
EST:     TACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGG                         TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT
genomic: TACCTTCAAAAACTGCAATTGCACCTGTTAACCCAACATTTTTGCCAAGGgtgagagtat ... tgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacattgtttactatttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
                          tgttaat  putative branch site (score: 3)
                         ttgttaattaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgttggtgctagaaatgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - gttggtg
- - - - - - - - - - - - - - - - - -cgtgccg
- - - - - - - - - - - - - - - - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa