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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatatctccttcatttaagtatgctaccttttcaacatttttgctggtgttaacttgggatgagaaggctggttgatgctggtgtttcttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCAAATTTCACCGATTTATTTGTCTATCGTATCGGCGGTGGCCCCCAAGCAC

Basic information

species Vitis vinifera
transcript Vv14s0066g02630.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G038588_T04 (Zea mays), 3'ss of exon 7
aaaatatctccttcatttaagtatgctaccttttcaacatttttgctggtgttaacttgggatgagaaggctggttgatgctggtgtttcttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCAAATTTCACCGATTTATTTGTCTATCGTATCGGCGGTGGCCCCCAAGCAC-----------------------------------------------------------
                                                      |   |   ||  || ||       | ||  |||      | | |||||||||||||||||  || ||||||||||||||||  |||| ||  ||   |||||||  ||| | |  || |||   ||||| |||||||  ||||| |                                                           
-----------------------------------------------------gatccgccttgttaaagccaa---gtcctaatgtgct---cctgcaggaatacttttatgggattgcaaatgatcttgcaccgcactcaaacattgtcaatttcagTGATGTCTCGGTGTATAAAATCGGTGGTGGCCATCAAGCTCCCCGTTCAGCATTACCTATCGGTGCAGAGCCTGTGGCAGATCCTACTCGACTTGTTGCT

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G038588_T02 (Zea mays), 3'ss of exon 7
aaaatatctccttcatttaagtatgctaccttttcaacatttttgct---ggtgttaacttgggat---gagaaggctggttgatgctgg----tgtttcttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCAAATTTCACCGATTTATTTGTCTATCGTATCGGCGGTGGCCCCCAAGCAC
      | | |||  ||      | ||||| || | |  |  ||| |    || | ||| |    |   ||   | || ||| | ||       |  |     | | |||||||||||||||||  || ||||||||||||||||  |||| ||  ||   |||||||  ||| | |  || |||   ||||| |||||||  ||||| |
------tgttcttagttct----tactaccgttacgaggtaattgttcactgtctgaaccttatcttttgatccgccttgttaaagccaagtcctaatgtgctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTCAATTTCAGTGATGTCTCGGTGTATAAAATCGGTGGTGGCCATCAAGCTC

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G38670.1 (Glycine max), 3'ss of exon 7
---aaaatatctccttcatttaagtatgctaccttttcaacatttttgctggtgttaact-tgggatgagaaggctggttgatgctggtgtttcttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCAAATTTCACCGATTTATTTGTCTATCGTATCGGCGGTGGCCCCCAAGCAC
       | ||  |  |        |  ||      |||| ||||    |     ||  | |||  | |     || | ||       || || |  ||  ||||||||||| ||||||||||||||||||||| | ||| | || ||| || ||||||| |  ||||| ||||| |||||  | || ||||| || || || |
tcttttctctcctcccccccctgacactcttaacactcaaaatttcccgttcaactatttatggcctaatggaacttgctgccatc--tgattttgact--cagGAATACTTCTATGGCCTTTCAAATGATCTTTCTCCACATTCTAATATTGCAAATTTTAGTGATTTGTTTGTTTATCGAGTTGGTGGTGGGCCACAGGCCC

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G43930.1 (Glycine max), 3'ss of exon 7
--aaaatatctccttcatttaagtatgctaccttttcaacatttttgctggtgttaacttgggatgagaaggctggttgatgctggtgtttcttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCAAATTTCACCGATTTATTTGTCTATCGTATCGGCGGTGGCCCCCAAGCAC
      | ||  |  |   |     |  || |  |   | |||||           | ||  | |   | ||    ||| ||||    |   ||     ||||||||||| ||||||||||||||||||||  | ||| | || ||| || ||||||| |  ||||| ||||| |||||  | || ||||| || || || |
cttttctctcctccccccctggcactcttaacactctgaaattttcctgttcaactatttttggtctaatgga-aattgctgctacc-tgattttgacacagGAATACTTCTATGGCCTTTCAAATGATCTATCTCCACATTCTAATATTGCAAATTTTAGTGATTTGTTTGTTTATCGAGTTGGTGGTGGGCCACAGGCCC

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|30130802|gb|CB916141.1|CB916141
EST:     TATCCAGGGGTGCAAAATTCCGTCAAAAGGCCAGGAGCTACAGGATAAGG                         GAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCA
genomic: TATCCAGGGGTGCAAAATTCCGTCAAAAGGCCAGGAGCTACAGGATAAGGgtaaatatca ... ttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCA
EST: gi|110398356|gb|EC964659.1|EC964659
EST:     TATCCAGGGGTGCAAAATTCCGTCAAAAGGCCAGGAGCTACAGGATAAGG                         GAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCA
genomic: TATCCAGGGGTGCAAAATTCCGTCAAAAGGCCAGGAGCTACAGGATAAGGgtaaatatca ... ttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtgttaacttgggatgagaaggctggttgatgctggtgtttcttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCAAATTTCACCGATTTATTTGTCTATCGTATCGGCGGTGGCCCCCAAGCAC
                                       tgtttcttccttcc  CT-rich tract
      ttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatatctccttcatttaagtatgctaccttttcaacatttttgctggtgttaacttgggatgagaaggctggttgatgctggtgtttcttccttccagGAATACTTTTATGGCCTTTCAAATGATCTTGCACCATACTCCAATGTTTCAAATTTCACCGATTTATTTGTCTATCGTATCGGCGGTGGCCCCCAAGCAC

aaaatat
- - - -ctccttc
- - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgctg