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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgctagagctgtaatgaatgttgaattttataaaaactgacaatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC

Basic information

species Vitis vinifera
transcript Vv08s0007g07400.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 9
---tgatgctagagctgtaatgaatgttgaatttt--ataaaaactgacaatgaatgtgc-acacatttgcatggta-gtaaaact--cggtggttttgtgacttg--cagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
    | | ||  |           || | ||||     ||||||   | |        |  |  ||   |  || |   | || ||   | || | |||||  |||  ||||||||||| |||||||||||||| |||||||| || |||||||| |||  ||| ||||||||| | |||||||  |||||||||||||||||||| | ||
gtaagttactgcacaatctccctgtgctaaattcagagtaaaaatgtaaagcagtcaggttaagcaagagactgatgcatgaagctgctgctgttcttgtggtttgttcagAACATTCAGGGTTTCATGTGGGACGAGGAGAAGGTGAACAATGAGCTGAAGACCTACATGACCCGTGGGTTCAGGGATGTGAAGGAGATGTGCAGGAGCC

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 9
tgatgctaga--gctgtaatgaatgttgaatttta--taaaaactgacaatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
 |    |||   ||| |     |   |||    |   |    || ||| |   |         ||||     || |  |      ||| ||| ||   || |||||||| || || ||||||||||| || ||||| ||||||   || |||||||||||||||||  | |  |||   || |||||| |||||||| | | ||
-gtcagtagctcgctcttgcccactgtgagccgtgcttccttacggactacatagcactgtgaatttaacccgtggacaccacacgtgctttcgtctgtt-cagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 9
-tgatgctagagctgtaatgaatgttgaatt-ttataaaaactgac-aatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
    ||||     |  |   | ||     || || || ||| | |  ||| ||| | | |   | || |        |   | |||| |||||||||   |||||||| ||||||||||||||||||||||||||||| |||||||| ||   ||| |||||||||| ||| ||||||||||||||||| ||||||| |||||
aaattgctcattttagaggaattgcatccttattgtacaaattaattaattaatataccc---tatgtagcccttacatggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 8
-tgatgctagagctgtaatgaatgttgaattttataaaaactgacaatgaatgtgcacacatttgcatggtagtaaaac--tcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
    ||||     |  |   | ||   |    |     |   |  ||| |||    | || |     | ||  | | |   | |||| ||||||| |   |||||||| ||||||||||||||||||||||||||||| |||||||| ||   ||| |||||||||| ||| ||||||||||||||||| ||||||| |||||
aaattgctcattttagaggaattgc--acccctgctgtacaggttaattaattaatatac-tccatgtagtccttacatggttggtgattttgtggcacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 9
tgatgctagagctgtaatgaat--gttgaattttataa--aaactgacaatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
   | || |||  ||    |||   || |  |||| ||  |   | ||        || |  ||||    |   | ||||    | |  || ||| |    |||||||||||||| |||||||||||||||||||| || ||||| || ||   ||| |||||||||| ||||||||||||||||||||| ||||||| |||||
---tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgtaatcattaaggtta-attaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 8
tgatgctagagctgtaatgaatgttgaattttataaaaactgacaatgaatgtgcacacatttgcatggtagtaaaact----cggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
     ||  ||  ||    |||  |   ||  ||| |   | |         || |  ||||   | | || | |||         |  || ||| ||   |||||||||||||| |||||||||||||||||||| || ||||| || ||   ||| |||||||| | ||||||||||||||||||||||||||||| |||||
--tcactttagtggttccaaattctt--ttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC

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|110695999|gb|EE074656.1|EE074656
EST:     TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAG                         AACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
genomic: TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAGgtatcatact ... tgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
EST: gi|110422698|gb|EC989026.1|EC989026
EST:     TTGAGTGGGTTCAG                         AACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
genomic: TTGAGTGGGTTCAGgtatcatact ... tgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
EST: gi|110422744|gb|EC989074.1|EC989074
EST:     TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAG                         AACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
genomic: TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAGgtatcatact ... tgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
EST: gi|33404831|gb|CF210458.1|CF210458
EST:     TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAG                         AACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
genomic: TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAGgtatcatact ... tgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
EST: gi|33404746|gb|CF210373.1|CF210373
EST:     TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGGTCAG                         AACATTCAAGGATTCATGTGATATGAGGAGAAA
genomic: TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAGgtatcatact ... tgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAA
EST: gi|110428368|gb|EC994837.1|EC994837
EST:     TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAG                         AACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG
genomic: TATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAGgtatcatact ... tgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
                        tagtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgctagagctgtaatgaatgttgaattttataaaaactgacaatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
tgatgct
- - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - -ctgacaa
- - - - - - - - - - - - - - - - - - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - cacacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtggtt