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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaatcactgatcttgagttgtttggttattttaatttgcctaccactcaattagaaatataatgtctatgcctgtatacatggaggactaggaataatttgctggttcattgctcttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC

Basic information

species Vitis vinifera
transcript Vv18s0001g08040.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G09580.1 (Glycine max), 3'ss of exon 1
gtaatcaatcactgatcttgagttgtttggttattttaatttgcctaccactcaattagaaatataatgtctatgcctgtatacatggaggactaggaataatttgctg-gttcattgctcttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC
                  ||   | |   || | |   |   |||   || ||||| |||          || | | |  |||     | |  |||   ||||||| || ||| | |||   ||  ||||||||| || ||||||||||||||||| || || |||||||||||||| ||  | ||||  ||||||||||||||| |||||   ||||| || || |   
---------------gtatgcactatgcagtgagtgaga---gccattcattcaatgagag---------ctgtacttacata-----atgtgtagatctaatttgttgtgttgaatgcatatc--acagATGGATAGAACATCTATACTTGGAGACACTATTGATTACATGAAAGAACTTCTGGAGAAGATCAACAATCTGCAGCAAGAAGTAGAAGTAGATTCAAACA

upper sequence: Vv18s0001g08040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G09670.1 (Glycine max), 3'ss of exon 1
gtaatcaatcactgatcttgagttgtttggttattttaatttgcctaccactcaattagaaatataatgtctatgcctgtatacatgg--aggactaggaataatttgctg-gttcattgctc-ttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC---
                       | |   || | |   | |       || ||||| || | |||| |  |    |   | |     |  | |   ||   |||||||  | ||| | ||||  |||| ||||||||| || ||||| ||||||||||| || || |||||||||||||| ||  | ||||  ||||||||||||||  ||| |   ||||| || || ||     
----------------------gtatgcagtgagtgagagtcatt---cattcaatgagtactatacttacagaactactttgttgtgttatgttcagatctaatttgtcgtgttgaatgcttattcttacagATGGATAGAACATCAATACTTGGAGACACTATTGATTACATGAAAGAACTTCTGGAGAAGATCAACAATCTGCAACAAGTA---GAAGTAGATTCAAGCATGG

upper sequence: Vv18s0001g08040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G36370.1 (Glycine max), 3'ss of exon 1
gtaatcaatcactgatcttgagttgttt--ggttattttaatttgcctaccactcaattagaaatataatg-tctatgcctgtatacatggaggactaggaataatttgctggttc---attgct-cttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC
|||   | | |       |||||  ||    |  ||  ||   ||   | |   ||  ||||| ||  ||| | | || |   ||| ||| || |  ||   ||||||||| |||    |||  | ||||| |||||||||||| ||| ||||||||||||| || || ||||| ||||| ||||| || || |  || || ||| || || ||||||  ||||| || ||||   
gtatgaagttagaa----tgagtcattatgagaaatactagaatgttaaac---cacatagaactactatggtttgtgtc---atatatgcagcataagtgctaatttgcttgttgtaaattaatgcttctcacagATGGACAGAACAGCTATACTTGGAGACACTATCGATTATATGAAGGAGCTCTTGGAAAAGATTAATAATTTGAAGCAAGAAATAGAAGTTGATTCCAACA

upper sequence: Vv18s0001g08040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G17900.1 (Glycine max), 3'ss of exon 3
gtaatcaatcactgatcttgagttgtttggttattttaatttgcctaccactcaattagaaatataatgtctatgcctgtatacatggaggactaggaataatttgctg-gttcattgctcttctaacagATGGACAGGACATCTATACTTGGAGA---TACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC-----
                             || | |   | |       || ||||| |||  | || |             |||||   |   |||   ||||||| || ||| | |||   ||  ||| ||||| || |||||||||||||||||   ||| || |||||||||||||| ||  | ||||  ||||||||||||||| |||||   ||||| || || |        
-----------------------------gtgagtgagagtcatt---cattcaatcagagttgtact-------------tacataatgtg-tagatctaatttgttgtgttgaatgcatatc--acaaatggatagAACATCTATACTTGGAGACAGTACTATTGATTACATGAAAGAACTTCTGGAGAAGATCAACAATCTGCAGCAAGAAGTAGAAGTAGATTCAAACATGGCA

upper sequence: Vv18s0001g08040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G65640.2 (Arabidopsis thaliana), 3'ss of exon 1
gtaatcaatcactgatcttgagttgtttggttattttaatttgcctaccactcaattagaaatataatgtctatgcctgtatacatggaggactaggaataatttgctggttcattgctcttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC
                       ||||      ||| |      ||||    |     ||||  | ||   |     |  |    |     | ||   || ||| |   |||||      |     ||||||||||||||||| ||| | |||||| |||||||||||||||||||||| ||||| | |||||||||  | || || ||  |  |||        | | 
-----------------------tgttcttacttttaagggaatctacagaaccggctgaaaagtgataaat-catttaaaagtgttttaaaataatgattattggtatgttcaaaaaaat-----cagATGGACAGGACATCGATATTAGGAGATGCCATAGATTACATGAAAGAGCTTTTAGACAAAATCAACAAATTACAAGATGAGGAACAAGAACTTGGAAATA

upper sequence: Vv18s0001g08040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G10570.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaatcaatcactgatcttgagttgtttggttattttaatttgcctaccactcaattagaaatataatgtctatgcctgtatacatggaggactaggaataatttgctggttcattgctcttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC
        ||||||||     ||| ||   || | | ||| ||| ||    |   |     | | ||||| |||   | |             |    || |||   |  |  | |          |||||||| |||||||| ||||| |||||| | |||||||||||||| ||||| || || |  || |||||  |||| |||||  |  |||        ||  
------gttcactgataaaaggttattgctttttgtgaatctgcatagagtttgttgtatgagaaaatgtatataatttt-------------tgatgattattatataataaaat----------cagATGGATAGGACATCGATACTAGGAGATGCAATAGATTACATGAAGGAGCTTTTGGACAAGATTAACAAGTTGCAAGAAGACGAACAAGAACTTGGAAGCA

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|161717518|gb|FC068506.1|FC068506
EST:     TGAATGACCGGCTTTCAATGCTAAGATCTGTTGTCCCCAAAATTAGCAAG                         ATGGACAGGACATCTATACTTGGAGATACGATAGA
genomic: TGAATGACCGGCTTTCAATGCTAAGATCTGTTGTTCCCAAAATTAGCAAGgtaatcaatc ... cttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGA
EST: gi|161720492|gb|FC070604.1|FC070604
EST:     TGAATGACCGGCTTTCAATGCTAAGATCTGTTGTCCCCAAAATTAGCAAG                         ATGGACAGGACATCTATACTTGGAGATACGATAGACTACATGAAAGAGCTA
genomic: TGAATGACCGGCTTTCAATGCTAAGATCTGTTGTTCCCAAAATTAGCAAGgtaatcaatc ... cttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgtatacatggaggactaggaataatttgctggttcattgctcttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC
                                    ttcattgctcttct  CT-rich tract
                       aataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaatcactgatcttgagttgtttggttattttaatttgcctaccactcaattagaaatataatgtctatgcctgtatacatggaggactaggaataatttgctggttcattgctcttctaacagATGGACAGGACATCTATACTTGGAGATACCATAGATTACATGAAAGAGCTATTAGAGAGAATCAACAATCTGCAGGAAGAAAATGAAGTGGACTCCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA