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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaagaaaaagactggtttctcttacagttatgacagcattctttagaagagttatcatccttgcaggattattctaatctctctttcaacatttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG

Basic information

species Vitis vinifera
transcript Vv18s0164g00070.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os08g07760.1 (Oryza sativa), 3'ss of exon 7
--------------------------------agaaaagaaaaagactggtttctcttacagttatg-acagcattc---tttagaagagttatcatccttgcagg-attattctaatctctctttcaacat-ttcagGAGGGAACA---GTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG
                                ||  || |  | || |  ||| | || || | | |    | | |     |   | |   |||    | |   |   || |||| |      |  |  ||| |||   |||||       |   || |||||||||||||| || ||||||||||| || || || |||||||||  |||||| ||||||||||||||||  || || ||
gtgagatctgttcatattcacagctgtgcaacagccaacactatgatttttttttgttgcactgacgcgtggtacttatgctggtatggactatggaacatattgttgttgttctgacaataataacctcatgttctatagGGAGTTCATCTAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGAGCAGCCTTGCTATTTGCTATTCCTGCTATTGGTTTTGCATGGTATCGGCGCAG

upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 7
-agaaaagaaaaagactggtttctcttacagttatgacagcattctttagaagagt---tatcatccttgcag------gat------tattctaatctctctttcaacatttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG---
  ||      | ||  |   |||| ||||| || ||| |    |    | | |  |    || |    |||||      |||      |||||   |     |      ||| ||  |||  ||      || |||||||||||||| ||||| ||||| | |||||| || || ||||| | ||| |||||||| |||||||||||||| ||  |   
gtgattctctatagttttaattctgttacatttgtgatactgcttgggatatgcatatgcataaatgatgcagacaggggatttgacatattcgggtggaattaattctattccatcagGTGACTCCAAAACTGGAGCAATTGCTGGAGGTGTTGCTGCAGCTGCTGCATTGCTGTTTGCGGTTCCGGCAATTGGATTTGCATGGTGGCGGCGGCGTAA

upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 7
agaaaagaaaaagactggtttctcttacagttatgacagcattct--ttagaagagttatcatccttgcaggattatt-ctaatctctctttcaacatttcagGAGGGAACAGTGCCA---CAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG
|  ||  |       |  ||| ||       |     || ||     | |  |  | |||    | |   |  || || || |  |||  ||     || ||||| | | |  | |||   | |||||||||||||| || |||||||||||||| || || |||||||||  |||||||||| ||||||| |  ||||| ||   
aataactaccttcttttttttgtccctaccctgcattagtatggcagtaattaaggctatggaacatatggctttgttactgacatcttatttt---ttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG---

upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G150024_T03 (Zea mays), 3'ss of exon 7
agaaaagaaaaagactggtttctcttacagttatgacagcattctttagaagagttatcatccttgcaggattattctaatctctctttcaacatttcag-
           ||  |  ||  |||     |  |  ||  | |      ||   ||| ||| || |  |    |||   |   ||   |  |   |  |     |||      || | | |||||||| ||||| ||||| |||||||||||||| ||  | ||||||| ||| |||||||  ||||||  |||||||||  |   
---------gtaggttttttaatctatttctattctcattactacactaaaactttagcattctggatgacacattgacactacttcctggattgtctactattagGTGCTTCTGGCCCTGGAGCAATCGCTGGAGGTGTTGCTGCTGGTGCTGCATTGGTTTTTGCTGTTCCAGCAATTGCATTTGCAATGTGGCGCCGTCGTAA

upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G115420_T01 (Zea mays), 3'ss of exon 7
agaaaagaaaaagactggtttctcttacagttatgacagcattctttagaagagttatcatccttgcaggattattctaatctctctttcaacatttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG---
         |     ||  |   |||  | ||     |  |  ||    ||   ||| |||  | |  |     | ||   ||   |||     |   |  |||      |  ||| |||||||| ||||| ||||| ||||||||||| || ||  | ||||||| |||||||||||  ||||||  |||||||||  |   
-------gtaggttttgaatctacttttattttcattaatacact---aaaactttagcattttggatgacacgtactt-cctggatttatgtctactattagGTGCTTCTAGCACTGGAGCAATAGCTGGAGGTGTTGCTGCTGGTGCAGCATTGGTGTTTGCTGTTCCTGCAATTGCATTTGCAATGTGGCGCCGTCGTAA

upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 7
agaaaagaaaaagactggtttctcttacagttatgacagcattctttagaagagttatcatccttgcaggattattctaatctctctttcaac---atttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG
    |   | | |  |  | | | | | | ||||||  ||| |  | | ||     || |      |||   |  || || ||  || |  |    ||| ||||||| ||  ||||||| |||||||| ||||| || || ||||||||||||||| || |||||||||| ||||||||||  ||||| |||||||| |||||
-tgcacctacatggtttatatttgt-atatttatgaatgcaatgctaaaaatgaagataaagaa-acagtgatgatccaaccttcctctatatctaattgcagGAGGTAATGGTGCCACCGGAGCAATAGCTGGAGGAGTTGCTGCTGGTGCTGCTCTATTATTTGCTGCACCTGCAATTGCATTTGCCTGGTGGCGTCGAAG

upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G36280.1 (Glycine max), 3'ss of exon 7
agaaaagaaaaagactggtttctcttacagttatg---acagcattctttagaagagttatcatccttgcaggattattctaatctctctttcaac---atttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG
        | | |  |  | | | | | | |||||    || || |    | ||     || |      |||   |  || || ||  || |  |    ||| |||| || ||  ||||||| |||||||| || || ||||| || |||||||||||| || |||||||||| ||||||||||  ||||| |||||||| |||||
-----cctacatggtttatatttgt-atatttatgtatgcaacactaaacataaagaagataaaagaaacagtgatgatccaaccttcctctatatcgaattgcagGGGGTAATGGTGCCACTGGAGCAATAGCCGGAGGTGTTGCCGCTGGTGCTGCTCTATTATTTGCTGCACCTGCAATTGCATTTGCCTGGTGGCGTCGAAG

upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G08360.1 (Glycine max), 3'ss of exon 5
agaaaagaaaaagactggtttctcttacagttatgacagcattctttagaagagttatcatccttgcaggattat--tctaatctctctttcaac--atttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG
      |     |           ||||| ||||   |    |  || |||   | |  ||    | || | |||  | | | || || |       ||| ||| ||| || |||||||| || ||||| ||||| || || ||||| ||||||||| |  |||||||||||||||||||||  ||||| |||||||| |||||
----ctgtttttgctacaacaactttacatttattttatatgttcttggaaacctcaagataaaagaagcactattgtttcaactttcctctgtttgattgcagAAGGAAATAGTGCCACTGGTGCAATAGCTGGAGGAGTAGCTGCAGGTGCTGCTCTGTTATTTGCTGCTCCTGCAATTGTGTTTGCTTGGTGGCGTCGAAG

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|71873068|gb|DT022123.1|DT022123
EST:     ATTTTCTCCACCTCCCCCATTTGTCCCACCACCACCAATTTCTTCACAAG                         GAGGGAACAGTGCCACAGGAGCAATTGCTGGAGGTGTGGCTGCTGGTGCTG
genomic: ATTTTCTCCACCTCCCCCATTTGTCCCACCACCACCAATTTCTTCACAAGgtaatcttcc ... aacatttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTG
EST: gi|37187909|gb|CF607260.1|CF607260
EST:     ATTTTCTCCACCTCCCCCATTTGTCCCACCACCACCAATTTCTTCACAAG                         GAGGGAACAGTGCCACAGGAGCAATTGCTGGAGGTGTGGCTGCTGGTGCTG
genomic: ATTTTCTCCACCTCCCCCATTTGTCCCACCACCACCAATTTCTTCACAAGgtaatcttcc ... aacatttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaagagttatcatccttgcaggattattctaatctctctttcaacatttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG
                             ttctaat  putative branch site (score: 2)
                                   tctctctttca  CT-rich tract
                         attattctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaagaaaaagactggtttctcttacagttatgacagcattctttagaagagttatcatccttgcaggattattctaatctctctttcaacatttcagGAGGGAACAGTGCCACAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - aagaaaa
- - - - - - - - - - - - - - - - - - - gcattct
- - - - - - - - - - - - - - - - - - - - - - - -agaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgca