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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT

Basic information

species Vitis vinifera
transcript Vv14s0171g00400.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 2
gtatgtcttttgtgtctttacaagagatagttgc-cttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattga-tcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
||  ||| |   | ||||    |     |  ||  |  |  |   | |   ||  | |        |  || | | |||   || | |||| | ||| |||||| |||||  | | | |  || | || ||||||||||| || || ||||| || ||||| ||||| ||||||||||||||||| || |||||  |||| 
gtcagtcctac-tatcttcttcatcttcatctgaacgaagaacacacgaacgaaccaa-------gaaattaatc-taactgaattcttgaatttttgcagGGGACCTGGCATCGCGGTGCTGATCCTGTCATGGATCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTC

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G149216_T01 (Zea mays), 3'ss of exon 2
gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaat-attgatctttt---------cagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
       |  |     | ||| || |||     | || | |  ||    | |||  |   | | | ||    | | |      ||  |||||  ||          |||||| |||||  | | | | ||| | || || ||||| || || || ||||| |||||||| ||||| ||||||||||||||||| ||||||||  |||| 
-------tgattcaattgtacgagcgattaactcgttgtcagataaagattatt--agggggtcacgggcagataaatggttcattgttgattattggcgtgcacacagGGGCCCTGGCATCGCGGTGATGATCCTGTCGTGGATAATCACCCTATACACGCTATGGCAGATGGTGGAGATGCACGAGATGGTGCCTGGGAAGCGGTTC

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G127338_T02 (Zea mays), 3'ss of exon 1
gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaa-atattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
||  ||    |      || | ||   |       |   |   |   |||||   |  || | | || |  | ||||  |    ||       | | |||||| || ||  | | | |  || |||| || |||||||| || || ||||| || ||||| ||||| ||||||||||||||||| || || ||  | || 
gtgcgtacgctag---cttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCGGGCAAGCGCTTC

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
---gtatg-tcttttgtgtctttacaagagatagt-tgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
   ||||  | |  ||   |||    |  | |||| |  |||  | ||| | |   | |   | |   |    ||||  || | ||   | |     | | ||||||||| |||||    ||| |  | || ||||||||||| || || ||||||||||||||||||||||||||||| || |||||||| || ||| |||||
atggtataatgtcatgaaacttcggcacggttagtgtaacttgcttttttt-ttaaactaagtgtttgttgatttgagaattacaa---tgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
---gtatgtcttttgtgtctttacaagagatagttgccttattatt-tatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
     ||| | |    |   | | || |||||     ||| ||| | ||| |   || | ||  | ||    || |    | ||  | |||   | |||||||||||||||||||     || |  | || ||||||||||| || || ||||| ||||||||||||||||||||||| || ||||| ||||| ||| | |||
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgtttt---ttaatttgagaatcactatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G24520.1 (Glycine max), 3'ss of exon 1
-----gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
       |   | ||   || | || |  |     ||   ||||             | | ||  | ||    || ||  | | ||  |   || | | ||||||||||| |||||     |  | || || ||||||||||||||  | ||||| |||||||||||||| |||||||| || ||||||||||| ||| | |||
tagataaacaacattatagtatatatactatgcgtttttgttatggaaagaaaaatgtactatgcgttt----tttaatttgagaatcactatgctttcttcagGGGTCCCGGTGTAACTGTGCTAGTCCTGTCATGGATCATTACCTTGTACACCCTATGGCAAATGGTAGAGATGCATGAAATGGTTCCTGGAAAACGTTTT

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
--gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataa-aaaaaatattgatcttt---tcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
  | ||  | | |||   |||  ||    |   | | | |  |||||  | |||||  ||| |  |||  ||    |||  | ||| | ||| | | |   | ||||| || ||  | |   |  || | ||||||||||| || || ||||||||  ||||||||||||| |||||||| ||||||||||| || ||| | |||
ttgaata-catatgtagttttttaatttcttactacataa--atttacttttgatttgattag--taatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
          |   |      ||   | |   |  ||||| |      || |  |   || || ||   | |||       || |  |  |||||||||||| || ||  | |   |  ||||  | |||||| |||| || || |||||| ||||||||||||| || ||||| || ||||||||||| ||  | |||
---------gtaaattcccctaaaccaaaaccggtttatttt----acctaaaccggatttatcaaatcttaaccggttttaatttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ10949 (Selaginella moellendorffii), 3'ss of exon 1
gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
                                          | | ||  ||    || | || | |  |  |  |   |    | ||  | ||| |||||| |||||  |  |  |  |  | || || |||| | | || || ||||| |||||||||||||| |||||||||||||||||    || ||  | || 
-----------------------------------------gtaacgttcga----atgttataacgtctacattttttagggttcttcgtttttccagGGGGCCTGGGATCTTCGTGCTCCTCCTCTCCTGGACCGTCACGCTCTACACGCTATGGCAAATGGTGGAGATGCACGAGATGGTGGAGGGCAAGCGCTTC

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|161719199|gb|FC065732.1|FC065732
EST:     GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATG                         GGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
genomic: GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATGgtatgtcttt ... atcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
EST: gi|161707654|gb|FC057408.1|FC057408
EST:     GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATG                         GGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
genomic: GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATGgtatgtcttt ... atcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
EST: gi|161718440|gb|FC067297.1|FC067297
EST:     GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATG                         GGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
genomic: GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATGgtatgtcttt ... atcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
EST: gi|161717137|gb|FC066560.1|FC066560
EST:     GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATG                         GGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
genomic: GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATGgtatgtcttt ... atcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
EST: gi|110724165|gb|EE099752.1|EE099752
EST:     GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATG                         GGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
genomic: GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATGgtatgtcttt ... atcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
EST: gi|110703326|gb|EE080072.1|EE080072
EST:     GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATG                         GGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC
genomic: GTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATGgtatgtcttt ... atcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
                                        tattgat  putative branch site (score: 3)
                                              tcttttc  CT-rich tract
                        ttgaacataaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG