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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccatgacaagcttcagggctttaaagatgtccatgcatgtgagaggagtcttatgtgcatgttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA

Basic information

species Vitis vinifera
transcript Vv01s0011g03280.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
---tccatgacaagcttcagggctttaaagatg-tccatgcatgtgagaggagtcttatgtgcatg-----ttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA
    |||   |    |  |    || ||   || | |    |||   ||  | |    ||  |||      |||     | || | |||| |         |||| ||||||||||||| |||| |  |||| ||||| || |||||||| || || || |||||||||||||| || ||||||||||| ||||||||||| ||||| |
agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttga---------tctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
---------------------------------------------------------tccatgacaagcttcagggctttaaagatgtccatgcatgtgagagg---agtcttatgtgcatg--ttcccctttcagaca----ttttaaataagcgattcttg-----------cagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA
                                                         |  | | |  | ||    ||| | |  |||        | |   ||     ||| | |  || ||   ||||  |||| | |     | |  ||  | || | |||           ||||||||||| | |||  | || |||||| | ||  |||| |||||||| || |||||||||||||| || ||||| || || ||||||||||| ||||| |
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 8
----tccatgacaagcttcagggctttaaagatgtccatgcatgtgagaggagtcttatgtgcatgttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA
       ||||     | |     | || |||  | ||     || | |      | | |   |    |   |   ||| || || |  |||  ||||||||||||||||||||   || | || || |||||  | ||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| ||||
agagcttatgatcttatgccaccttctatagagatgcaga---gtaaaaatcacataacgaaaaaaa-cttttcaaagatatgttgatcaagtcattcttgcagGTTATTGGAATCAATTTGTTATCTCAATCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTTCGACTTGCAATAATAGAATATA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 8
tccatgacaagcttcagggctttaaagatgtccatgcatgtgagaggagtcttatgtgcatgttcccctttca--gacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA
   ||   |||| | | | ||  | |     | || |     | |   ||   | |   | |    ||||| |  ||||||||||  ||   ||||||||||||||| ||||  ||||| || || || ||  | ||||| ||||||||||||||||| |||||||| ||||||||||| || |||||||| ||||| ||||
-ttatt-taagccttatgtctgcataccaccctatactcacaaaacatgtacaaagcaaaagaaaacctttgaaagacattttaatcaatgtattcttgcagGTTATAGGAATCGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
--tccatgacaagcttcagggctttaaagatgtccatgcatgtgagaggagtcttatgtgcatgttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA
  |  ||   |  ||| | | |   | |     | || |     | |        |   | |   |    |   |||||||||||  ||   ||| ||||||||||| |||| |||||| || || || ||  | ||||| ||||||||||||||||| |||||||| ||||||||||| || |||||||| ||||| ||||
cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttt--tggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
tccatgacaagcttcagggctttaaagatgtc-catgcatgtgagaggagtcttatgtgcatgttcccctttcagacatt--ttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA
                  | ||     || || | ||  ||    ||        | |     ||||   || ||    |   | ||| | |  ||   |||||||||||||| ||||||| | || |||||| | |||||||||||||| || ||||| |||||| | || ||||| || ||||||||||||||||||||| 
------------------gtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG

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|110390370|gb|EC955275.1|EC955275
EST:     TTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAATCAG                         GTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAG
genomic: TTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAATCAGgtttgtcata ... attcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAG
EST: gi|351038699|gb|FQ464565.1|FQ464565
EST:     TTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAATCAG                         GTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAG
genomic: TTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAATCAGgtttgtcata ... attcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAG
EST: gi|30303438|gb|CB980232.1|CB980232
EST:     ACTAAATATCATTAGCAAGCTTGATCAAATAAATCAG                         GTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAG
genomic: ACTAAATATCATTAGCAAGCTTGATCAAATAAATCAGgtttgtcata ... attcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtcttatgtgcatgttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA
                                              ttcttgc  CT-rich tract
                           agacattttaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccatgacaagcttcagggctttaaagatgtccatgcatgtgagaggagtcttatgtgcatgttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
-ccatgac
- - - - - -cttcagg
- - - - - - - - - - - - - - - -ccatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataag