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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA

Basic information

species Vitis vinifera
transcript Vv11s0016g00530.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 3'ss of exon 3
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattac--cctggtgtttcttctcattcat-atatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
   | |||  |          ||   |  ||   | | || ||  |  ||  | ||   |||    ||   ||   | |||   || ||| || | | ||||||||||||||| | ||||||||||||||||| |||||| | |   |||  || || || |||||||| ||| |||| || || ||||| ||||| ||||||
--tttttatctgttggctcatgtgtgattttggttataaagtccatgttgttt-tattctacaatttgaacttgaatatcaaatattataatttaatttgcagGATATCTGTGACTTTTGTTGATAAGGATGGCGAGGAAAAGCTTGTTAAAGTACCTATAGGAATGTCAATGCTAGAGGCAGCACATGAGAATGACATAGAA

upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 4
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgc-----agGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
     |||      | ||    |      || |||| ||    ||  |||  |  | |  | ||   |  || |||| ||    | ||||  ||||||     ||||| |||||  |||||||  | ||||||||    || ||    || || |||||  |||||||||| || ||||||||||||||||||||||| || |||
---ctttaaaggggcttctccttcagtttttccctcctaggaaatagctg--tccaaaacaaccgattaatttttctaatgagcaaatttctttgtgctgcacagGATCTCTGTAACATTTGTGAACAAGGATGGCACAGAGCAGACAATCAGTGTCCCTGTTGGAATGTCCATCTTAGAAGCTGCTCATGAAAATGACATCGAA

upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G013607_T02 (Zea mays), 3'ss of exon 4
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttc---tcattcatatatttaat-tgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
 | | ||| | |    | |  |||   | ||   |   || |  ||   | |     | | | ||| || || ||    | |||  | |   || | ||  ||| || || ||  |||||||  | ||||||||    ||| |    ||  | || ||  |||||||||| ||||||||||||||||||||||| || ||||| 
-agttttactgaattgttagtgttgagctttcaat---aattatttagggtagaagcagtcctctgatgattgttgaggttatttttctccatactgtgaacagAATCTCGGTAACATTTGTCAACAAGGATGGCTCAGAAAAGACAATATGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAACGACATAGAG

upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 3
caatcttagttacacatc-atggttctacatttcctcttaactcatttctgcatgtagattac-cctggtgtttcttctcattcatatatttaa--ttgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
  |       | |||| | |  ||| ||| ||| ||| ||  |  || ||  |||   ||    | |  |    || || | |  |  |   ||  || ||||||||||||||  | ||| ||||||||||||| |||||  | || || |  |||||  ||||||||||||||||||||||||||||||||||||| || |||
--agacagaatgcacaacgactgttgtac-tttgctcgtatatt-ttactagatggcaatagtgcatcattccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA

upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G05130.1 (Glycine max), 3'ss of exon 3
---caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
     || | | |    |||||||    |  |||       ||   |     |     || ||  | |  || | |||    ||   |      ||| ||||||||||||||  | ||| |||||||||| || |||||  | || || |  |||||  |||||||||||||||||||||||||||||||||| || ||||||
actagatgtcaatagtgcatcatgtgagtttattaaaaaaaaaaaaaaaga-gagcacag-ttgtcattctgctccttactttttg-aggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAA

upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G07780.1 (Glycine max), 3'ss of exon 1
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgta-gattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
||    || |     | | || || ||   |     || | | |       ||| |   ||  | |  || | |||    ||   |      ||| ||||||||||||||  | ||| |||| |||||||| |||||  | || || |  |||||  |||||||||||||||||||||| ||||||||||| || || |||
cacaactactattgtaccttgcttatatcatgtgagtttattaaaaaaaaaatgcacagttgtcattctgctccttactttttg-aggcaacattatgcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA

upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G05450.1 (Arabidopsis thaliana), 3'ss of exon 4
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
                  | | | ||||      | || |  ||   ||| |   | |||  |     |||| |  | ||||   | |||       ||||||| |  |    |||||||||||||| |||||||||  ||   |||  || || |||||||||||  || | |||||||||||||||||||||||||| 
----------------gtaagttactac-cgaaatattcatccagcgctgaagcaatatttgctgatagtttatcataattctgttgtttt------cagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGAC

upper sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G21090.2 (Arabidopsis thaliana), 3'ss of exon 4
-caatcttagttacacatcatggttc-tacatttcctcttaac--tcatttctgcatgtagattaccctggtgtttct-tctcattcatatatttaat----tgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
  |   | |  |  |  |||     | | ||  || |   |||    |    ||     | |  || || |  |   | |   || ||| |||||  |    | | |||||||   ||  | ||||||||||| ||||||||||||  ||| || | ||| ||  | ||||||   ||  | |||||||||||||||||||||||||||
gtaggttcaaatttatctcagaaaacattcaactcttgacaacaacgaaaaatgagacaacagcactctcgcctgaatgtaagatacatgtatttcgtatttttttcagGATAAACGTTACCTTTGTTGATAAAGATGGAGAGGAAATTCATATCAAGGTTCCAGTAGGAATGAACATCCTTGAAGCTGCTCATGAAAATGATATAGAA

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|110379961|gb|EC945192.1|EC945192
EST:     ACCACAGCTGCTGACAACCATTCTGGGGAGGAGAATGAAGAGGAAGAAAC                         GATATCCGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGT
genomic: ACCACAGCTGCTGACAACCATTCTGGGGAGGAGAATGAAGAGGAAGAAACgtaagctctg ... aattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGT
EST: gi|30252686|gb|CB970237.1|CB970237
EST:     AGCTGCTGACAACCATTCTGGGGAGGAGAATGAAGAGGAAGAAAC                         GATATCCGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGT
genomic: AGCTGCTGACAACCATTCTGGGGAGGAGAATGAAGAGGAAGAAACgtaagctctg ... aattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGT
EST: gi|71887854|gb|DT036909.1|DT036909
EST:     ACCACAGCTGCTGACAACCATTCTGGGGAGGAGAATGAAGAGGAAGAAAC                         GATATCCGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGT
genomic: ACCACAGCTGCTGACAACCATTCTGGGGAGGAGAATGAAGAGGAAGAAACgtaagctctg ... aattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
                                         atttaat  putative branch site (score: 4)
                            ttctcattcatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - -acacatc
- - - - - - - - - - - - - -catttcc
- - - - - - - - - - - - - - - - - - - aactcat
- - - - - - - - - - - - - - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taccctg