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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagacatttaaggtttgaattcattatgtggaaatgataatgagtgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT

Basic information

species Vitis vinifera
transcript Vv14s0068g01530.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g70100.1 (Oryza sativa), 3'ss of exon 1
-ttagacatttaaggtttgaattcattatgtggaaatgataatgagtgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
  | ||    | |    || ||    | | |  ||    |  || |  |||   |  |        | ||   || | | |   |  |   |  | | ||| | ||| |||||||||||||| ||||||||||||||||||  |||||  ||    | ||||| ||||| ||  | || || |   |  | || ||| | |
gctggagtgatgatagctgtatgagatct-tcaaatcacttctgcgaatttaagaagtaggaaggtgtgattgcagcttatagcttttgtttctttttcagGTGTTTGTTCTTCAGGGGAGGTTTATATTTGGACCCGATGCAAGATCCTTGTACGTCACCATGTTCCTCATCATCGCGCCAGCGTCAATCTTTTGTTTGT

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 1
ttagacatttaaggtttgaattcattatgtggaaatgataatgagtgttt-tttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
                                     | | |   | |   |||||  | |||   ||  | |   |||   ||| || | ||   |||||| |||||||||||| || ||| | ||||||||||| ||||| ||||| |||| |||||| ||  | |||||||||||||||||| | |||||||||||||
-----------------------------------gtacagtttctatccatttatgactatgag-ggtgcttattcattgcttttatcattttcttgcagAAATTTTTTCTTCAAGGAAGGTTCATATTTGGACCAGATGTGAGATCACTGGCGCTGACAATTATTCTTATTGTTGCTCCTGTTGCAGTTTTCTGTGTCT

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 1
ttagacatttaaggtttgaattcatt----atgtggaaatgataatgagtgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
||||    | | | |   |||| |||    |||||  | || |    |||| ||||  || |  ||      || |   ||    |||||    ||  ||||||| ||||||||||||||| ||| | ||||||||||| ||||  |||||  |||  ||||| || || ||||||| |||||||||| | |||||||||||||
ttagtggctgatgctgcaaatttatttgaaatgtgctattgtt--ctagtggtttt-gttactgtgaa-aatacttattcactgttttcacccatttcctgcagAAATTTTTTCTTCAGGGCAGGTTCATATTTGGACCAGATGCAAGATCATTGGCCCTGACAATTTTTCTTATTGCTGCTCCTGTTGCAGTTTTCTGTGTCT

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G05670.1 (Glycine max), 3'ss of exon 1
ttagacatttaaggtttgaattcattatgtggaaatgataatgagtgttttttatttccatgctcggg---acgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
  |||||  |     ||| |||  |||| || ||    | |    |  | |  ||||        | |    | |   |||   ||| || | ||   |||||| |||||||||||| |||||| | ||||||||||| ||||| ||||| ||||  ||||| ||  | ||||| |||||||||||  | |||||||||||||
--agacaaatgttaattgcatt-gttatttgaaatatgttacagtttctatccatttatgactatgagggtgcttattcattgctttgataattttcttgcagAAATTTTTTCTTCAAGGGAGGTTCATATTTGGACCAGATGTGAGATCACTGGCACTGACAATTATTCTTATCGTTGCTCCTGTCGCAGTTTTCTGTGTCT

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 1
ttagacatttaaggtttgaattcattatgtggaaatgataatgag-tgttttttatttccatgctcggg-acgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
||||    | | | |   | || ||| ||   |  || |  ||   || |  |||| |   ||        | |   |||   ||||||   ||  ||||||| ||||||||||||||| ||| | ||||||||||| ||||  |||||  |||  ||||| || || ||||||| |||||| ||| | |||||||||||||
ttagtggctgatgctgcaactttatt-tg-aaatgtgctgctgttctggtggttatgttactgtgaaaatgcatattcattgttttcatccatttcctgcagAAATTTTTTCTTCAGGGAAGGTTCATATTTGGACCAGATGCAAGATCATTGGCCCTGACGATTTTTCTTATTGCTGCTCCCGTTGCAGTTTTCTGTGTCT

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 1
--ttagacatttaaggtttgaat--tcattatgtggaaatgataatgagtgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
  |     |||       || ||  |  || | |       ||| |  ||  |    | || |     ||||  ||     |  |  |  ||| ||   |||||||||| ||||||||||| ||| || ||||||| || ||||||||||| |||| ||||||||| |  || |||| ||  ||||||||  |||||||  |||
gctggtgtattgttttcctggatgattcttgtttttggggaatactttgttctcgaaagtttctctaccgggctgtttattttcgcgtt-ttattt---tgcagATATTCTTTCTTCAGGGAAGGTTTGTATTTGGGCCAGATGTTAGATCACTGGCGCTGACCATTTGTCTCATTGCTGTCCCTGTTACAATTTTCTGCATCT

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G41060.2 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------ttagacat--ttaaggtttgaattcattatgtggaa-atgataatgagtgtttttta--tttccatgctcgggacgtcaccatctgtttca------ttacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
                                            ||| |  |  || ||   | |  |  |    |  || ||  | | |  ||||  |||  |     | | |     || | ||| | ||  |      |  | | |||||||||||||| |||||| || ||| |||| || || || ||||| ||||| || || |||||||||   |||||||| || ||||||||  |||||||  |||
gttatatagttgatgctgtctgtatattgctttcaatgtcgaatttaaatctggtttagtagtaacctagtggaattaaacattttgaggtttgttccttaaatccttctacccaaagtgttaacatattttctaaatttgtcccatttctgcagATATTTTGTCTTCAAGGAAGGTTTATCTTCGGGCCGGATGTAAGATCACTTGGTCTGACCATAAGTCTTATTGTGGCACCTGTTACAATTTTCTGCATCT

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 1
ttagacatttaaggtttgaattcattatgtggaaatgataatgagtgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
||||   |       | ||||| |  || | ||  |            |  || |  |||   |    || |          ||  |  | | |||||||||||||| |||||| || ||| |||| || || || ||||| ||||| || || |||||||||   |||||||| || ||||||||  |||||||  |||
ttagtagtaacctagtggaattaaacattttgaggtttgttccttaaatccttctacccaaagtgttaacatattttctaaatttgtcccatttctgcagATATTTTGTCTTCAAGGAAGGTTTATCTTCGGGCCGGATGTAAGATCACTTGGTCTGACCATAAGTCTTATTGTGGCACCTGTTACAATTTTCTGCATCT

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|161706260|gb|FC055445.1|FC055445
EST:     CAAGTGGTTCGGATGCTTTACGAACTTACCAGACCTGGAAAGGCAGCAAT                         ATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTG
genomic: CAAGTGGTTCGGATGCTTTACGAACTTACCAGACCTGGAAAGGCAGCAATgtaagcccag ... ttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTG
EST: gi|294966639|gb|GW839630.1|GW839630
EST:     CAAGTGGTTCGGATGCTTTACGAACTTACCAGACCTGGAAAGGCAGCAAT                         ATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTG
genomic: CAAGTGGTTCGGATGCTTTACGAACTTACCAGACCTGGAAAGGCAGCAATgtaagcccag ... ttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT
                                            cttgtct  CT-rich tract
     tttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagacatttaaggtttgaattcattatgtggaaatgataatgagtgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT

- - - - - - - - - - - - - - - -gaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccatc