C-It-Loci: A knowledge database for tissue-enriched loci.

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main


C-It-Loci is a tool that contains four types of data: "Conserved Regions", “Genes", “Transcripts", and "Expressed Transcripts". Three of these are searchable/browseable via their corresponding links. Each row within these pages links to a page containing RNA-seq data from a variety of tissues with other useful data. Each data type can be accessed by clicking the corresponding link on the navigation bar at the top of the page. This will direct to the page containing search form and a table of entries. See Browsing and Searching below for directions on navigating and searching C-It-Loci.

Conserved Regions

CGP: “C-It-Loci Genome Position”, which is a region in which pairs of adjacent homologous protein-coding genes shared between one or more species.

UCNEbase: regions defined by the database for ultra-conserved non-coding elements (UCNEs) called “UCNEbase” (http://ccg.vital-it.ch/UCNEbase/). For details about UCNEbase, please see: Dimitrieva S, Bucher P (2013) UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res 41(Database issue):D101-9.

VISTA: loci that are +/-300kb from the regions defined by the VISTA Enhancer Browser (http://enhancer.lbl.gov). For details about the VISTA Enhancer Browser, please see: Visel A, Minovitsky S, Dubchak I, Pennacchio LA (2007) VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res 35(Database issue):D88-92.

Quick Search

It is advised to use C-It-Loci's advanced search. However, in many cases, simplified search offers a useful and simple graphical method to search and to compare data. Upon submission, quick search will return Venn diagrams displaying the numbers of conserved regions, protein-coding transcripts, and lncRNA transcripts.
  1. Select tissue 1 (Required) - Specifies the primary tissue for the search, which is shown as the blue circles of the Venn diagrams on the left.
  2. Select expression 1 (Required) - Determines the type of expression shown by the Venn diagrams.
  3. Select tissue 2 (Optional) - Allows for comparing a secondary tissue to the primary tissue, which is shown as orange circles on the right of Venn diagrams.
  4. Select expression 2 (Optional) - Determines the type of expression shown by the Venn diagrams.
  5. GO - Clinking this button will submit the query.
To preform a quick search, the top selection boxes for a tissue and expression type must contain a tissue and expression value. The second row of tissues and expression types is optional, however, both must be set for the form to be valid. Note: the 'GO' button will be disabled if the form is not valid.

Advanced Search

The advance search allows for greater control of search results by allowing queries based on various types of data included in C-It-Loci. The advance search uses a query tag combined with a search string to specify the type of data to return. Additionally, the output of these queries can be combined together using the boolean operators: “and", “or", “not", and “()”. Note, if a query contains a space, then quotation marks should be added around the full string. If no tag is present in the query, it will be treated as an accession number or gene name. Again, if any spaces are included within the string, the entire string will be treated as multiple queries unless surrounded by quotation marks. See the table below for the types of queries:
Expression Example Description
No tag. CIL_000001 When no tag is specified the query is treated as an accession or gene name
SPECIFIC:(tissue) SPECIFIC:Heart Returns transcripts detected in only one type of tissue.
ENRICHED:(tissue) ENRICHED:Heart Returns transcripts which have increased expression in the given tissue.
EXPRESSED:(tissue) EXPRESSED:Heart Returns transcripts expressed in the given tissue type.
FPKMGT:(FPKM) or FPKMGT:(FPKM):(tissue) FPKMGT:5 or FPKMGT:5:Heart Returns transcripts with expression greater than the given FPKM. If a tissue is passed this will return transcripts with expression greater than the given FPKM in the given tissue.
FPKMLT:(FPKM) or FPKMLT:(FPKM):(tissue) FPKMLT:5 or FPKMLT:5:Heart Returns transcripts with expression less than the given FPKM. If a tissue is passed this will return transcripts with expression less than the given FPKM in the given tissue.
POS:(tax_id):(chromosome):(start)-(end) POS:9606:1:914880-969309 Returns regions, genes, or transcripts falling withing the given position.
BIOTYPE:(biotype) BIOTYPE:lincRNA Returns regions, genes, or transcripts which contain a transcript annotated as the given biotype.
REGIONTYPE:(CGP|UCNEbase|VISTA) REGIONTYPE:UCNEbase Returns regions which contain the given region type. If searching for genes or transcripts, genes and transcripts contained within the given region type will be returned.
TAXID:(7955|9606|10090) TAXID:7955 Returns regions, genes, or transcripts associated with the given taxonomy. Taxonomy IDs (TAXID) are: 7955 (zebrafish), 9606 (human), and 10090 (mouse).
GO:(GO term accession) GO:0005515 Returns regions, genes, or transcripts which contain an annotation of the given Gene Ontology (GO) term.
Boolean Operators
and TAXID:7655 and TAXID:10090 Returns accessions existing between two query sets.
or BIOTYPE:lincRNA or BIOTYPE:antisense Returns accessions existing in either of two query sets.
not not TAXID:9606 Returns accessions not in the query.
()BIOTYPE:lincRNA and (TAXID:7955 and TAXID:10090 and not TAXID:9606) or (TAXID:9606 and TAXID:7955 and not TAXID:10090) Increases the precedence of a query.
* gata* Specifies where to use wildcards in query. Note: wildcards are only supported for tagless searches.


The large size of C-It-Loci necessitates breaking queries into manageable sizes. This is accomplished via the browsing view. The browsing view breaks queries into pages of a given number of rows and allows navigation between pages via the “Previous” and “Next” buttons. Navigation to a desire page is also possible by setting the page number field to the desired page.

  1. The number of rows to show per page.
  2. Displays the number of the current page. When changed this will redirect to the new page number
  3. Move to the previous page.
  4. Move to the next page.

Record Pages

Record pages contain detailed information about a data type contained within C-It-Loci. This can include annotation data, genomic coordinates, expression data, homologs, and GO terms depending on the data type.

Genome Browser

Each record page will contain at least one genome view. C-It-Loci uses the Biodalliance genome browser. For details about this browser, please refer to http://www.biodalliance.org/

Visualization of Transcript Expressions

There are two ways to view expression data: a graphical view and a text view. Users can toggle between the two views using the provided buttons. The text view is a simple table comparing various transcript expressions versus tissues with numerical values representing the average FPKM values followed by the standard deviations with ± symbol. The graphical view scales the FPKM values using the equation y = 100.0 - (log(x)+12)*((3*x)/(x+1)+1), where y is the lightness value in the HSLA color.

  1. bed file with conserved regions - Download
  2. All expression data:

Data sources

Study AccessionSample AccessionRun Accessiontax_idInstrument ModelLibrary LayoutAgeTissueENSEMBL Transcripts Detected
ERP000447SAMEA782568ERR0231447955Genome Analyzer IIPAIREDAdult Brain 16936
ERP000447SAMEA782570ERR0231457955Genome Analyzer IIPAIREDAdult Heart 10856
ERP000447SAMEA782572ERR0231467955Genome Analyzer IIPAIREDAdult Kidney 13547
ERP000447SAMEA782568ERR0231477955Genome Analyzer IIPAIREDAdult Brain 16602
ERP000447SAMEA782572ERR0231497955Genome Analyzer IIPAIREDAdult Kidney 13198
ERP000447SAMEA782570ERR0231507955Genome Analyzer IIPAIREDAdult Heart 11439
ERP000447SAMEA782568ERR0355457955Genome Analyzer IIPAIREDAdult Brain 23167
ERP000447SAMEA782570ERR0355467955Genome Analyzer IIPAIREDAdult Heart 23476
ERP000447SAMEA782572ERR0355477955Genome Analyzer IIPAIREDAdult Kidney 24427
SRP012040SAMN00849374SRR45307710090Genome Analyzer IIPAIREDAdult Ovary 23673
SRP012040SAMN00849374SRR45307810090Genome Analyzer IIPAIREDadult-8wksOvary 23249
SRP012040SAMN00849374SRR45307910090Genome Analyzer IIPAIREDadult-8wksOvary 21858
SRP012040SAMN00849374SRR45308010090Genome Analyzer IIPAIREDadult-8wksOvary 23178
SRP012040SAMN00849374SRR45308110090Genome Analyzer IIPAIREDadult-8wksOvary 23421
SRP012040SAMN00849374SRR45308210090Genome Analyzer IIPAIREDadult-8wksOvary 22867
SRP012040SAMN00849374SRR45308310090Genome Analyzer IIPAIREDadult-8wksOvary 22952
SRP012040SAMN00849374SRR45308410090Genome Analyzer IIPAIREDadult-8wksOvary 22586
SRP012040SAMN00849374SRR45308510090Genome Analyzer IIPAIREDadult-8wksOvary 23071
SRP012040SAMN00849374SRR45308610090Genome Analyzer IIPAIREDadult-8wksOvary 23121
SRP012040SAMN00849375SRR45308710090Genome Analyzer IIPAIREDAdult Breast 21881
SRP012040SAMN00849375SRR45308810090Genome Analyzer IIPAIREDadult-8wksBreast 24261
SRP012040SAMN00849375SRR45308910090Genome Analyzer IIPAIREDadult-8wksBreast 24505
SRP012040SAMN00849375SRR45309010090Genome Analyzer IIPAIREDadult-8wksBreast 22846
SRP012040SAMN00849375SRR45309110090Genome Analyzer IIPAIREDadult-8wksBreast 22780
SRP012040SAMN00849375SRR45309210090Genome Analyzer IIPAIREDadult-8wksBreast 23724
SRP012040SAMN00849379SRR45311610090Genome Analyzer IIPAIREDAdult Adrenal 21591
SRP012040SAMN00849379SRR45311710090Genome Analyzer IIPAIREDadult-8wksAdrenal 21496
SRP012040SAMN00849379SRR45311810090Genome Analyzer IIPAIREDadult-8wksAdrenal 21494
SRP012040SAMN00849379SRR45311910090Genome Analyzer IIPAIREDadult-8wksAdrenal 21648
SRP012040SAMN00849379SRR45312010090Genome Analyzer IIPAIREDadult-8wksAdrenal 21854
SRP012040SAMN00849379SRR45312110090Genome Analyzer IIPAIREDadult-8wksAdrenal 21502
SRP012040SAMN00849382SRR45313010090Genome Analyzer IIPAIREDAdult Adipose 24279
SRP012040SAMN00849382SRR45313110090Genome Analyzer IIPAIREDadult-8wksAdipose 24709
SRP012040SAMN00849382SRR45313210090Genome Analyzer IIPAIREDadult-8wksAdipose 23737
SRP012040SAMN00849382SRR45313310090Genome Analyzer IIPAIREDadult-8wksAdipose 23366
SRP012040SAMN00849384SRR45314010090Genome Analyzer IIPAIREDAdult Testis 27217
SRP012040SAMN00849384SRR45314110090Genome Analyzer IIPAIREDadult-8wksTestis 27203
SRP012040SAMN00849384SRR45314210090Genome Analyzer IIPAIREDadult-8wksTestis 27106
SRP012040SAMN00849384SRR45314310090Genome Analyzer IIPAIREDadult-8wksTestis 26915
SRP012040SAMN00849385SRR45314410090Genome Analyzer IIPAIREDAdult Kidney 24230
SRP012040SAMN00849385SRR45314510090Genome Analyzer IIPAIREDadult-8wksKidney 24150
SRP012040SAMN00849385SRR45314610090Genome Analyzer IIPAIREDadult-8wksKidney 22884
SRP012040SAMN00849385SRR45314710090Genome Analyzer IIPAIREDadult-8wksKidney 24114
SRP012040SAMN00849385SRR45314810090Genome Analyzer IIPAIREDadult-8wksKidney 23974
SRP012040SAMN00849385SRR45314910090Genome Analyzer IIPAIREDadult-8wksKidney 23895
SRP012040SAMN00849386SRR45315010090Genome Analyzer IIPAIREDAdult Liver 20467
SRP012040SAMN00849386SRR45315110090Genome Analyzer IIPAIREDadult-8wksLiver 19505
SRP012040SAMN00849386SRR45315210090Genome Analyzer IIPAIREDadult-8wksLiver 20444
SRP012040SAMN00849386SRR45315310090Genome Analyzer IIPAIREDadult-8wksLiver 20987
SRP012040SAMN00849386SRR45315410090Genome Analyzer IIPAIREDadult-8wksLiver 20716
SRP012040SAMN00849386SRR45315510090Genome Analyzer IIPAIREDadult-8wksLiver 21090
SRP012040SAMN00849387SRR45315610090Genome Analyzer IIPAIREDAdult Lung 24819
SRP012040SAMN00849387SRR45315710090Genome Analyzer IIPAIREDadult-8wksLung 24701
SRP012040SAMN00849387SRR45315810090Genome Analyzer IIPAIREDadult-8wksLung 24290
SRP012040SAMN00849387SRR45315910090Genome Analyzer IIPAIREDadult-8wksLung 24146
SRP012040SAMN00849389SRR45316610090Genome Analyzer IIPAIREDAdult Colon 22852
SRP012040SAMN00849389SRR45316710090Genome Analyzer IIPAIREDadult-8wksColon 22767
SRP012040SAMN00849389SRR45316810090Genome Analyzer IIPAIREDadult-8wksColon 22144
SRP012040SAMN00849389SRR45316910090Genome Analyzer IIPAIREDadult-8wksColon 23415
SRP012040SAMN00849389SRR45317010090Genome Analyzer IIPAIREDadult-8wksColon 23206
SRP012040SAMN00849389SRR45317110090Genome Analyzer IIPAIREDadult-8wksColon 23291
SRP012040SAMN00849390SRR45317210090Genome Analyzer IIPAIREDAdult Heart 22709
SRP012040SAMN00849390SRR45317310090Genome Analyzer IIPAIREDadult-8wksHeart 22627
SRP012040SAMN00849390SRR45317410090Genome Analyzer IIPAIREDadult-8wksHeart 23192
SRP012040SAMN00849390SRR45317510090Genome Analyzer IIPAIREDadult-8wksHeart 23164
SRP012040SAMN01164133SRR56748210090HiSeq 2000 PAIREDAdult Bladder 26140
SRP012040SAMN01164133SRR56748310090HiSeq 2000 PAIREDadult-8wksBladder 25423
SRP012040SAMN01164134SRR56748410090HiSeq 2000 PAIREDAdult Placenta 26598
SRP012040SAMN01164134SRR56748510090HiSeq 2000 PAIREDadult-8wksPlacenta 27056
SRP012040SAMN01164135SRR56748610090HiSeq 2000 PAIREDEmbyro Liver 24957
SRP012040SAMN01164135SRR56748710090HiSeq 2000 PAIREDE18 Liver 24380
SRP012040SAMN01164140SRR56749610090HiSeq 2000 PAIREDEmbyro Liver 25628
SRP012040SAMN01164140SRR56749710090HiSeq 2000 PAIREDE14.5 Liver 22850
SRP012040SAMN01164141SRR56749810090HiSeq 2000 PAIREDEmbyro Brain 26181
SRP012040SAMN01164141SRR56749910090HiSeq 2000 PAIREDE14.5 Brain 27856
SRP012040SAMN01164143SRR56750210090HiSeq 2000 PAIREDEmbyro Liver 25365
SRP012040SAMN01164143SRR56750310090HiSeq 2000 PAIREDE14 Liver 24369
SRP017959SAMN01886753SRR6493629606Illumina Genome IixSINGLEAdult Testis 44064
SRP017959SAMN01886754SRR6493639606Illumina Genome IixSINGLEEmbyro Placenta 32522
SRP017959SAMN01886755SRR6493649606Illumina Genome IixSINGLEAdult Ovary 34352
SRP017959SAMN01886761SRR64937210090Illumina Genome IixSINGLEAdult Ovary 27504
SRP017959SAMN01886762SRR64937310090Illumina Genome IixSINGLEEmbyro Placenta 24487
SRP017959SAMN01886763SRR64937410090Illumina Genome IixSINGLEEmbyro Placenta 24700
SRP017959SAMN01886764SRR64937510090Illumina Genome IixSINGLEAdult Testis 27413
SRP019807SAMN01984805SRR7872709606Illumina HiSeq 2000PAIREDNA Bladder 25830
SRP019807SAMN01984806SRR7872719606Illumina HiSeq 2000PAIREDNA Brain 28033
SRP019807SAMN01984807SRR7872729606Illumina HiSeq 2000PAIREDNA Breast 27519
SRP019807SAMN01984808SRR7872739606Illumina HiSeq 2000PAIREDNA Colon 26932
SRP019807SAMN01984809SRR7872749606Illumina HiSeq 2000PAIREDNA Heart 26587
SRP019807SAMN01984810SRR7872759606Illumina HiSeq 2000PAIREDNA Kidney 22583
SRP019807SAMN01984811SRR7872769606Illumina HiSeq 2000PAIREDNA Liver 27075
SRP019807SAMN01984812SRR7872779606Illumina HiSeq 2000PAIREDNA Lung 26862
SRP019807SAMN01984813SRR7872789606Illumina HiSeq 2000PAIREDNA Muscle 19319
SRP019807SAMN01984814SRR7872799606Illumina HiSeq 2000PAIREDNA Ovary 26467
SRP024369SAMN02951650SRR8914957955Illumina Genome Analyzer IIxPAIREDAdult Heart 25049
SRP024369SAMN02951649SRR8915047955Illumina Genome Analyzer IIxPAIREDAdult Liver 22481
SRP024369SAMN02951652SRR8915107955Illumina Genome Analyzer IIxPAIREDAdult Muscle 24932
SRP024369SAMN02951648SRR8915117955Illumina Genome Analyzer IIxPAIREDAdult Brain 24478
SRP017959SAMN02265389SRR9433409606Illumina HiSeq 2000SINGLEEmbyro Placenta 26721
SRP017959SAMN02265388SRR9433419606Illumina HiSeq 2000SINGLENA Ovary 31273
SRP017959SAMN02265387SRR94334210090Illumina HiSeq 2000SINGLEAdult Ovary 24365
SRP017959SAMN02265390SRR94334310090Illumina HiSeq 2000SINGLEAdult Ovary 24233
SRP017959SAMN02265391SRR94334410090Illumina HiSeq 2000SINGLEEmbyro Placenta 24454
SRP017959SAMN02265393SRR94334510090Illumina HiSeq 2000SINGLEEmbyro Placenta 24388
SRP017959SAMN02265400SRR94335510090Illumina HiSeq 2000SINGLEEmbyro Placenta 27713
SRP017959 SAMN01886760SRR64937110090Illumina Genome Analyzer IixSINGLEAdult Brain 26157