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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaacataatgcctacctaaaaagaggaagtcattgtctttgcatacactgaatttatctatttatgtgtttgcaataatcaaactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA

Basic information

species Vitis vinifera
transcript Vv08s0007g07240.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 13
ttaacataatgccta--cctaaaaagaggaagtcattgtctttgcatacactgaatttatctatttatgtgtttgcaataatca-aactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA
 |  |||  |  |||  | ||     |   ||   |  |  ||   |   ||   ||| |   ||  ||    | || |  |     |  |||  ||  |||||| |||||||| || || ||||||||||| || || || ||||||||||||||| |||| ||||||||||| ||||| ||||| ||
cttgcatgttttctagtcttagttctattgagctgtgttgattattt---cttgttttgttgtttactgctcattcatttcttgtgtcattttaatttggcagGGAAAAGATAAGACTGCTGAAGAGAGAAGGATAGCTATCTGTATATTTGATGATATTGCAGAGCAATGTCGTGAATCTGCTCTCAA

upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 13
------ttaacataatgcctacctaaaaagaggaagtcattgtctttgcatacactgaatttatctatttatgtgtttgcaataatcaaactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA--------------
      ||     | |    ||||     ||||      |  ||| |   |     |  |||||   | ||| |  ||    ||  |      |||  ||  |||||| |||||||||||  | ||||||||||| || || || ||||| |||||||||||||| |||||||| || ||||||||||| ||              
gcgtcttttttccattcttaacctgttgtgaggtgcatctattctatatttttttgggttttat---tctatctcattttggta-ccttgtggtttattt--gcagGGAAAAGATAAAACACCTGAAGAGAGAAGGATAGCTATCTGTATTTTTGATGATGTTGCAGAGCAATGCCGTGAATCAGCTCTGAAGTATTATGACACAT

upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 12
----------------------------------------------------------------------------------------------------ttaacataatgcctacctaaaaagaggaagtcattgtctttgcatacactgaatttatctatttatgtgtttgcaataatcaaactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA
                                                                                                    |  |  || | |||  || || |    |  | | ||   |     | | ||  |  |   |      | | | || |  |  |||| |   |  ||  |||||||  ||||| |  | ||||| ||||| |||||||| || || |||||||||||||||||||| || || ||| ||||  ||| 
gtaagtgagatgatgaaccattggatttggtgcattttctttgcttgttagggttgtgacttgtgagcactgaacaatacatcacaatttgatgtcactctagatttattacct--ctgaacatgaaacataaatgcactattgaatattgg-taaactaaacaccatatgtacatt--tttaactttccaccaatttagGGTAAGAATAAATCACCAGAAGAAAGAAGGATTGCCATATGCATTTTTGATGATGTTGCTGAGCATTGCCGTGAAGCAGCAGTTAG

upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 13
ttaacataatgcctacctaaaaagaggaagtcattgtctttgcatacac-tgaatttatctatttatgtgtttgcaataatcaaactct----ttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA
     | | |  |||  |    | ||   | ||| |  |   ||||      | | | | |  | ||    || |  |  ||     ||    ||   ||  ||||||||||| |||||  | || || || ||||||||||||||||||||||||||||||||||||||  |||| ||| | ||||||||
-----acactttctaagtttgtacagatggccatagcttagacatatttgccattctgttttctgatccaattcccctcctcccctactgatattcaataatcagGGTAAAGACAAAACCTCAGAGGAAAGGAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCATGGTCGTGAAGCTGCTCTTAA

upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 13
----ttaacataatgcctacctaaaaagaggaagtcattgtctttgcatacactgaatttatctatttatgtgtttgcaataatcaaactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA
    || |  |  ||   |  |    |   |     |     ||  ||| |  |    | ||||| ||     | | |  || | | | ||  |  |    ||||||||||| |||||  | || || || ||||||||||||||||||||||||||||||||||||||  |||| ||| | ||||||||
actttttaagttttgtacaggtggccatttgcttagacatatttgccattctgttttctgatctaattccccttctcccttattgatattcaataat----cagGGTAAAGACAAAACCTCAGAGGAAAGGAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCACGGTCGTGAAGCCGCTCTTAA

upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S31_225V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------------------ttaacataatgcctacctaaaaagaggaa-gtcattgtctttgcatacactgaatttatctatttatgtgtttgcaataatcaaactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA
                                                                | ||||  | | |   ||   | |     |  |  | || | | |      | || ||        || |  |  || ||  |  | ||    | || ||||||||||    ||  | || || |||||| ||||||||||  | || ||||||||||||||||||||| | ||  | ||  ||||
gtgcgtcctcctgtcctgtgaagttcttaatttttaatttattttgcttatttacaatggtgtattacattttccttcattatcgaaatacttgctacagactgtccttttgtcaacttgattgtcgagcgtttaagttatcattga-ttattactctgtgtagGGTAAAGAACGCACTCCTGACGAAAGAAGAGTTGCCATTTGCGTTTTCGATGATGTTGCTGAGCAATGTGGCGACGCTGCGATTAA

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|37184053|gb|CF603407.1|CF603407
EST:     CTTTCTTGCCTTTCTTTGATGAGCTTTCATCTTACCTGATGCCTATGTGG                         GGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGAT
genomic: CTTTCTTGCCTTTCTTTGATGAGCTTTCATCTTACCTGATGCCTATGTGGgtaagtttaa ... gcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactgaatttatctatttatgtgtttgcaataatcaaactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA
                                       ctctttgctt  CT-rich tract
      aatttatctatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaacataatgcctacctaaaaagaggaagtcattgtctttgcatacactgaatttatctatttatgtgtttgcaataatcaaactctttgcttatgcagGGTAAAGATAAAACGGCCGAAGAGAGAAGAATTGCCATTTGTATATTTGATGATGTTGCTGAGCAATGTCGAGAATCAGCTCTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - taatgcc
- - - - - - - - - aaaaaga
- - - - - - - - - - - - - - - -cattgtc
- - - - - - - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa