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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaatgacttgtgttgttgatagagtgtggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG

Basic information

species Vitis vinifera
transcript Vv14s0068g01280.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 8
tgtgaatgacttgtgttgttgatagagtgtggctattgttgtttccttccaatgttaaattttggtaat-tttattttta-----tatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
  |   ||  || ||| |||       | |  || |  ||  |||||    |  ||   ||||  |  |  | | || ||     |  ||| |   | | || ||||| ||||| ||||||||||| || |||||||| |||||||||| |||||| || |||||||||||  | || ||||| ||| ||
--ttgttgggttttgtggtttgc----tttttctttgattcattcctcgtgaacttgtgttttcatggtgctcagttgtaattgcttacataaaactattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 8
tgtgaatgacttgtgttgt-tgatagagtgtggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagt-ttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
  |   |  ||   ||| | || |    || |    || |||  | ||| |  | |   || |   |  | ||  || |  |   | | | ||    | ||||| ||||| ||||||||||| || |||||||| |||||||||| |||||| ||||||||||||||  | || ||||| ||| ||
gctttgttgctgtggttatatggtttgctgagttggtttttgccttctttctctttcgtatgtcatt--tcttgcttgtgaactgtaactattactgtacagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATCCTTAGATATGGTCTCCCTCCATCATTCCTG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 8
-tgtgaatgacttgtgttgttgatagagtgtggctatt-gttgtttccttccaatgttaaattttggtaattttatttttatatcatgagt-ttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
 ||| |||    | | |   ||  | |   | | ||||  | ||    ||   ||| |    | |     | ||  || |  |   | | | || |  | ||||| ||||| ||||||||||| ||||||||||| ||||||||||  ||||| || |||||||||||  |||| ||||| ||| ||
atgttaata---tatttcactggcacaaccttgttatttatggtgaaattaatatggtggtatctcaatttcttggttgtgaactgtaattattattgtgcagGTATTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTGTCTTTGTGGAGAGCATTCTTAGATATGGTCTGCCGCCATCATTCCTG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 8
---tgtgaatgacttgtgttgttgatagagtgtggctattgttgtttccttccaatgtta-aattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
   | |       || | |   | |     | |   | |  |||||  | |  |||| ||   |  |  |    |  ||||||  | ||    || | |   |||||||||| ||||||||||| ||||||||||| ||| | ||||| ||||| || || ||||||||  |||| ||||||||||||
acttttctcgcgtttttatcactcaccacatattcttgtc-ttgttatcctaaaatgctatggtccttattcactactttttactttata---tttttccaaagGTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 8
---tgtgaatgacttgtgttgttgatagagtgtggctattgttgttt-ccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
   |   |     |  ||   || ||    |     | |     |||  |   |||   | | | ||| | | |   ||||||  | ||    || |     |||||||||| ||||||||||| ||||||||||| ||| | ||||| ||||| || || ||||||||  |||||||||| ||||||
atttactagcatttgttgaccttaattttatacttttctcaccttttatcactcaacacttattcttgctcactac-tttttactttata---ttttttcaaagGTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCACCATCTTTCTTG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
-------tgtgaatgacttgtgttgttgatagagtgtggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
       ||||||| | || |||  |   | | |  || |   |||| |        |||| |     |       ||| || || | || |   |||| |||  |||||||||||||||||||||| |||||||| || ||||| ||| | ||||| || || ||||||||  | |||||||| ||||||
cataaaatgtgaataagttctgtgatctcttgtgcttgccc--tgttatcgta----aatgctgtgactcttctgatttgttattttttcttttttttc-cctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 8
----tgtgaatgacttgtgttgttgatagagtgtggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
    ||| ||  | || |||  |   |   |  || |   |||| |          ||| |   ||  |   | |||||||||  || |   ||| ||||  |||||||||||||||||||||| |||||||| || ||||| ||| | ||||| || || ||||||||  | |||||||| ||||||
aaaatgttaacaagttctgtgatctcttctgcttgccc--tgttatcataaat-gctgtgactcttctgatttgttatttttacttctttt-tttttcctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACTGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
tgtgaatgacttgt-gttgttgatagagtg-tggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
            || | | |  | | | || |    || | | ||  |||  |||   | |  |     | | | |||| || |   |   | |  ||  ||||||||||||||||||||||||| |||||||| |||   || || ||||| ||  | ||||| || || || ||  | ||||||
------------gtaggtatctacacattgctctgaatagatattctcttgtaatacaatacct----gaatctgttttgatctt-cggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG

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|110364030|gb|EC927670.1|EC927670
EST:     AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAG                         GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
genomic: AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
EST: gi|45770351|gb|CN006203.1|CN006203
EST:     TTGC-ATGGTGCT-TACCAG-TAT-GGGAG                         G-TTTCAGCTCCTGGATGCA-TTTTGTGCTGTACGTGT-TTTGCAGAGAGT
genomic: TTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
EST: gi|349827680|gb|FQ422548.1|FQ422548
EST:     AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAG                         GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
genomic: AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
EST: gi|110699022|gb|EE077184.1|EE077184
EST:     AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCGGTTATGGGGAG                         GTTTTCAGCTCCTGGATGCATTTTTGGGCTG
genomic: AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTG
EST: gi|110688297|gb|EE066689.1|EE066689
EST:     AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAG                         GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
genomic: AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
EST: gi|351022393|gb|FQ445168.1|FQ445168
EST:     AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAG                         GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
genomic: AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
EST: gi|351013608|gb|FQ429749.1|FQ429749
EST:     AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAG                         GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
genomic: AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
EST: gi|71887796|gb|DT036851.1|DT036851
EST:     AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAG                         GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT
genomic: AAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgtaattttcc ... tctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG
                                           tttctccttc  CT-rich tract
     aatgttaaattttggt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaatgacttgtgttgttgatagagtgtggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG

- - - tgacttg
- - - - - - - - - - - - - - -tggctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgagt