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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacatttttttcttttggtgcaaattctcaagtttttaccaaaattcttgcttctatatgatatttatttatgatttgttttacaattgctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCCTCTTTG

Basic information

species Vitis vinifera
transcript Vv05s0049g01220.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 11
--acacatttttttcttttggtgcaaattctcaagtttttaccaaaa-ttcttgcttctatatgatatttatttatgatttgttttacaattgctcctta-cagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCCTCTTTG
  | | |   ||| |||||   |    || |    |||||||||    || ||| |||   ||   | || | | | |   ||  |     ||  | ||| ||||||||||||||||||||||||| ||| | ||||| || || || ||||| || ||||
aaagagagcatttccttttttcgt---ttttttcatttttaccatctctttttgattcatcattgcacttctct-tcacaagtaatttttgtgtacattatcagCTGAATTGAAGAAGAAGAGCACAAAACCTAAAAGACCATCTATTAAGTCACTATTTG

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G35110.2 (Glycine max), 3'ss of exon 11
-acacattt-ttttcttttggtgcaaattctcaagtttttaccaaaattcttgcttctatatgatatttatttatgatttgttttacaattgctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCCTCTTTG
   |  ||  ||  |        | || | |   ||| ||  | ||||   |   ||  | |  || |   |||  |     | |     || |  |  ||||||||||||||||||||||||| ||| | ||  | || || || ||| |||| ||||
gttattttgattaccccccaacaccaaatttattgttcttttccaaatagatttatcattgtactaatc--ttaacaagcaatatgggtatgttgttatcagCTGAATTGAAGAAGAAGAGCACAAAACCTAAGCGACCATCTATTAAGACCCTATTTG
















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|18459729|gb|BM438007.1|BM438007
EST:     TAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAG                         CTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCC
genomic: TAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAGgtatctatct ... ctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCC
EST: gi|32245340|gb|CD711159.1|CD711159
EST:     TAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAG                         CTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCC
genomic: TAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAGgtatctatct ... ctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCC
EST: gi|110700396|gb|EE078384.1|EE078384
EST:     CACGTATAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAG                         CTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCC
genomic: CACGTATAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAGgtatctatct ... ctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCC
EST: gi|71879891|gb|DT028946.1|DT028946
EST:     CACGTATAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAG                         CTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCC
genomic: CACGTATAAGAACTTTGAAATTGTAAATGATCAGCCAGTACCTGGGATAGgtatctatct ... ctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgcttctatatgatatttatttatgatttgttttacaattgctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCCTCTTTG
                                          ttgctcctt  CT-rich tract
       ttctatatgatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacatttttttcttttggtgcaaattctcaagtttttaccaaaattcttgcttctatatgatatttatttatgatttgttttacaattgctccttacagCTGAATTGAAGAAGAAGAGCACCAAAACCAAAAGGCCCTCCATCAAGTCCCTCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - tggtgca
- - - - - - - - - - - - - - - - - - -taccaaa