cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000000183

Region for Gene ENSMUSG00000000183 (MGI Symbol: Fgf6)

This page describes one promoter-based search region.

Page Contents

Overview
Genomic Context
Image of Motifs and Modules
Motifs Found in this Region

Search region overview
Search region location	chr6:127,038,762-127,040,972 (+) (2211 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Gene name	Fgf6
Ensembl gene ID	ENSMUSG00000000183
Gene description	fibroblast growth factor 6 [Source:MarkerSymbol;Acc:MGI:95520]
Gene description source	MGI Symbol
Modules (Co-occurring motif patterns)	11 annotation-based module(s) No 'de novo' modules exist in this database.

Genomic Context: Mouse genome assembly from Dec 2005. (UCSC mm7, NCBI m35, Ensembl v38)

The image shown below was created to provide context for this search region by showing a 100000 bp span of the genome, centered on this search region.

The first track shows the location of the search region in red.
The last track shows known gene locations in this 100000 bp span of the genome.

This promoter-based search region is located close to a particular gene of interest, described in the table below. Click on the gene id to open a page at ensembl.org with more information about this gene.

Target gene used to create this search region
Ensembl ID	ENSMUSG00000000183 (Fgf6)
Ensembl Transcript ID	ENSMUST00000000187
Gene description	fibroblast growth factor 6 [Source:MarkerSymbol;Acc:MGI:95520]
Gene type	protein_coding
Gene location	chr6: 127,040,773-127,049,905 (+) (9,133 bp)
Distance from the region's midpoint to TSS	-904

The distance from a cisred search region to a gene, is measured from the center of the search region to either the transcription termination site (TTS) or the transcription start site (TSS), whichever is closer.
A distance is negative if the TTS/TTS is downstream of the search region's center, relative to the gene's strand.
A distance is positive if the TTS/TTS is upstream of the search region's center, relative to the gene's strand.

A transcript's location is always reported relative to the positive strand.

Image of Motifs and Modules

The image shown below illustrates the location of the motifs and modules within this search region.
However, the number of modules in a region may exceed the genome browser's track limit. Thus, for each type of module (pattern), the text in the yellow box below indicates whether or not any modules of that type exist, and if so, whether or not all the modules of that type are displayed. (If it indicates that only the top 20 modules are displayed, this ranking is based on the number of instances of each module.)

User-specified filter settings do not affect the features displayed in the UCSC genome browser view.

About the patterns shown in this image:
There are no 'de novo' patterns to show.
All instances of each (TRANSFAC) annotation-based pattern are shown.
There are no (JASPAR) annotation-based patterns to show.

Click on the image to view this region at UCSC.

This image uses the Mouse genome assembly from Dec 2005. (UCSC mm7, NCBI m35, Ensembl v38) and contains a number of custom tracks followed by several UCSC tracks. The custom tracks show:

The long red and gray bar at the top shows the nominal 'search region' within which comparative genomics discovery methods were applied. Motif predictions were not made in coding exons and most types of repeats. In this database, the locations of masks applied to the search region are shown in gray.

The numbered brown blocks are 'atomic' motifs, i.e. conserved DNA sequence motifs that were identified by discovery methods and post-processing operations. Motifs are shaded to indicate the discovery p-value; a darker motif was more significant at the discovery stage.

Following the motif discovery stage, motifs were filtered by membership in co-occurring patterns, and patterns were ranked by genome-scale properties. Motifs instances that occur in highly-ranked putative regulatory modules may be more reliable predictions of functional genomic elements.

The connected sets of blue boxes are co-occurring patterns, i.e. putative regulatory modules. Modules are shaded to indicate the number of times that a pattern is found in the target genome; a darker module is associated with more search regions. An pattern is called either 'de novo' or annotation-based, depending on the type of groups that appear in the pattern. (see next point)

Before patterns (i.e. modules) can be identified from atomic motifs, groups of similar motifs must be found; modules are then identified as co-occurring 'group labels' that satisfy certain criteria. Such groups can be identified a) by annotating atomic motifs with known binding site resources from TRANSFAC, JASPAR or ORegAnno; or b) by 'de novo' clustering. Currently we show both types of patterns, but we consider annotation-based groups and patterns to be more reliable than 'de novo' groups and patterns. Work to improve genome-scale 'de novo' grouping is ongoing.

Motifs Found in this Region

The contents of the table below can be modified by changing your filter settings.
Currently, this table only contains motifs which:
+ have a discovery p-value < 0.1
+ were found using any of these algorithms: MotifSampler, Consensus.oops, Consensus.omops, Consensus.zmops, MEME.tcm, MEME.oops, MEME.zoops

Showing 40 out of 40 atomic motifs.

Group(s) crtMmus#(name) [p-value]	Motif craMmus#	Discovery p-value	Location	Width	(+)motif	(-)motif
2 annotated group(s): 200006 (aMEF-2) [1.95E-04] 200006 (aMEF-2) [4.07E-04]	258	7.14E-02	chr6:127,038,793-127,038,805	13	GAACTATAAAGAT	ATCTTTATAGTTC
0 annotated groups	296	7.14E-02	chr6:127,039,078-127,039,089	12	nTkGmATGwCAG	CTGsCATkCmAn
2 annotated group(s): 200810 (SRF) [2.29E-04] 200805 (LEF-1) [7.65E-04]	326	7.14E-02	chr6:127,040,231-127,040,243	13	GCyCAryyTGGGT	ACCCArryTGrGC
1 annotated group(s): 201001 (DEAF-1) [3.81E-04]	354	7.14E-02	chr6:127,040,337-127,040,348	12	nTkGmATGACAG	CTGTCATkCmAn
1 annotated group(s): 200328 (Pax-8) [3.85E-05]	385	3.85E-02	chr6:127,040,405-127,040,417	13	TGGCCCTGGGACA	TGTCCCAGGGCCA
0 annotated groups	420	2.79E-03	chr6:127,040,416-127,040,432	17	srsGkTAwTkTTAsrGC	GCywTAAmAsTAmCwyw
1 annotated group(s): 200999 (AIRE) [5.77E-04]	492	2.79E-03	chr6:127,040,459-127,040,473	15	TTTTTAGGGCCATTA	TAATGGCCCTAAAAA
2 annotated group(s): 200999 (AIRE) [5.77E-04] 200721 (CACCC-binding_factor) [6.55E-04]	458	2.79E-03	chr6:127,040,461-127,040,470	10	GGCAwGGTGG	CCACCsTGCC
1 annotated group(s): 200242 (PPAR-alpha) [7.92E-04]	563	2.79E-03	chr6:127,040,543-127,040,555	13	CrGCATGGCGGCA	TGCCGCCATGCyG
1 annotated group(s): 200242 (PPAR-alpha) [7.92E-04]	529	2.79E-03	chr6:127,040,544-127,040,553	10	GGCATGGyGG	CCrCCATGCC
1 annotated group(s): 200538 (HTF) [9.51E-04]	596	7.14E-02	chr6:127,040,556-127,040,568	13	AGAGAksGTCCCy	rGGGACwmTCTCT
5 annotated group(s): 200059 (YY1) [4.61E-04] 200665 (Sp3) [4.75E-04] 200235 (AhR) [6.05E-04] ...	677	2.79E-03	chr6:127,040,570-127,040,577	8	CGCCATGC	GCATGGCG
5 annotated group(s): 200059 (YY1) [4.61E-04] 200665 (Sp3) [4.75E-04] 200235 (AhR) [6.05E-04] ...	625	2.79E-03	chr6:127,040,571-127,040,578	8	GsCATGGT	ACCATGwC
4 annotated group(s): 200059 (YY1) [4.61E-04] 200235 (AhR) [6.05E-04] 200235 (AhR) [6.56E-04] ...	655	2.79E-03	chr6:127,040,572-127,040,579	8	mCrTGGTC	GACCAyGk
0 annotated groups	712	7.14E-02	chr6:127,040,593-127,040,605	13	GCTCAGCCTGGGT	ACCCAGGCTGAGC
0 annotated groups	747	7.14E-02	chr6:127,040,614-127,040,626	13	kCyCAACCCGrGT	ACyCGGGTTGrGm
2 annotated group(s): 200807 (Egr-1) [8.66E-04] 4000 (FoxA1) [9.65E-04]	784	7.14E-02	chr6:127,040,627-127,040,639	13	GCCCGAwGCAGGC	GCCTGCsTCGGGC
4 annotated group(s): 200707 (TFIIA) [6.95E-05] 200983 (Bach1) [2.18E-04] 200684 (XPF-1) [2.61E-04] ...	849	2.79E-03	chr6:127,040,636-127,040,663	28	AGGCTTTGGTTTCATGT...	GAAGGCTGCTGACATGA...
1 annotated group(s): 4000 (FoxA1) [9.65E-04]	813	7.14E-02	chr6:127,040,644-127,040,655	12	GTTTCATGTCAG	CTGACATGAAAC
0 annotated groups	881	7.14E-02	chr6:127,040,665-127,040,677	13	TCTGCCTTCCAAA	TTTGGAAGGCAGA
4 annotated group(s): 200006 (aMEF-2) [1.49E-04] 200406 (MEF-2A) [2.26E-04] 200026 (RSRFC4) [5.35E-04] ...	1026	1.64E-03	chr6:127,040,671-127,040,685	15	TTCCAAAAATAAGCC	GGCTTATTTTTGGAA
4 annotated group(s): 200006 (aMEF-2) [1.49E-04] 200406 (MEF-2A) [2.26E-04] 200026 (RSRFC4) [5.35E-04] ...	918	1.64E-03	chr6:127,040,674-127,040,681	8	CAAAAATA	TATTTTTG
4 annotated group(s): 200006 (aMEF-2) [1.49E-04] 200406 (MEF-2A) [2.26E-04] 200026 (RSRFC4) [5.35E-04] ...	956	1.64E-03	chr6:127,040,675-127,040,682	8	AAAAATAA	TTATTTTT
5 annotated group(s): 200623 (Crx) [9.84E-05] 200006 (aMEF-2) [1.49E-04] 200406 (MEF-2A) [2.26E-04] ...	991	1.64E-03	chr6:127,040,676-127,040,681	6	AAAATA	TATTTT
5 annotated group(s): 200739 (E2F-4_DP-2) [3.91E-04] 200740 (Rb_E2F-1_DP-1) [4.05E-04] 200651 (NF-muE1) [6.54E-04] ...	1253	2.79E-03	chr6:127,040,684-127,040,701	18	yCCywGysGsCATGsyGr	yCrwCATGwCwrCsrGGr
3 annotated group(s): 200739 (E2F-4_DP-2) [3.91E-04] 200740 (Rb_E2F-1_DP-1) [4.05E-04] 200737 (E2F-1_DP-2) [8.65E-04]	1069	3.85E-02	chr6:127,040,686-127,040,697	12	CCTGCCGCCATG	CATGGCGGCAGG
4 annotated group(s): 200739 (E2F-4_DP-2) [3.91E-04] 200740 (Rb_E2F-1_DP-1) [4.05E-04] 200803 (DP-1) [8.61E-04] ...	1100	2.79E-03	chr6:127,040,688-127,040,697	10	TGCCGCCATG	CATGGCGGCA
5 annotated group(s): 200739 (E2F-4_DP-2) [3.91E-04] 200740 (Rb_E2F-1_DP-1) [4.05E-04] 200651 (NF-muE1) [6.54E-04] ...	1131	2.79E-03	chr6:127,040,689-127,040,698	10	GCCGCCATGC	GCATGGCGGC
4 annotated group(s): 200739 (E2F-4_DP-2) [3.91E-04] 200740 (Rb_E2F-1_DP-1) [4.05E-04] 200651 (NF-muE1) [6.54E-04] ...	1160	2.79E-03	chr6:127,040,690-127,040,699	10	CCrCCATGCC	GGCATGGyGG
2 annotated group(s): 200651 (NF-muE1) [6.54E-04] 200803 (DP-1) [8.61E-04]	1193	2.79E-03	chr6:127,040,691-127,040,698	8	CGCCATGC	GCATGGCG
0 annotated groups	1218	2.79E-03	chr6:127,040,692-127,040,699	8	GCCATGCC	GGCATGGC
12 annotated group(s): 200406 (MEF-2A) [2.10E-05] 200006 (aMEF-2) [3.15E-05] 200006 (aMEF-2) [1.08E-04] ...	1506	2.79E-03	chr6:127,040,710-127,040,746	37	AAACAAGAAGGGCGGTA...	AGAATTAATGGCCCTAA...
8 annotated group(s): 200406 (MEF-2A) [2.10E-05] 200006 (aMEF-2) [3.15E-05] 200006 (aMEF-2) [1.08E-04] ...	1288	1.64E-03	chr6:127,040,723-127,040,734	12	GkTATTTTTAGG	CCTAAAAATAmC
9 annotated group(s): 200406 (MEF-2A) [2.10E-05] 200006 (aMEF-2) [3.15E-05] 200006 (aMEF-2) [1.08E-04] ...	1319	1.64E-03	chr6:127,040,724-127,040,731	8	kTATTTTT	AAAAATAm
9 annotated group(s): 200406 (MEF-2A) [2.10E-05] 200006 (aMEF-2) [3.15E-05] 200006 (aMEF-2) [1.08E-04] ...	1356	1.64E-03	chr6:127,040,724-127,040,733	10	kTATTTTTrG	CyAAAAATAm
9 annotated group(s): 200406 (MEF-2A) [2.10E-05] 200006 (aMEF-2) [3.15E-05] 200006 (aMEF-2) [1.08E-04] ...	1392	1.64E-03	chr6:127,040,725-127,040,730	6	TATTTT	AAAATA
9 annotated group(s): 200406 (MEF-2A) [2.10E-05] 200006 (aMEF-2) [3.15E-05] 200006 (aMEF-2) [1.08E-04] ...	1434	1.64E-03	chr6:127,040,725-127,040,732	8	TATTTTTA	TAAAAATA
1 annotated group(s): 200436 (IPF1) [4.26E-04]	1470	2.79E-03	chr6:127,040,734-127,040,739	6	GGCCAT	ATGGCC
15 annotated group(s): 200985 (Stra13) [1.87E-04] 200449 (ZIC2) [2.50E-04] 200466 (HIF-1) [3.71E-04] ...	1538	2.79E-03	chr6:127,040,740-127,040,766	27	TAATTCTGACCACGTGC...	TGCCTCTCAGGCACGTG...
1 annotated group(s): 200761 (DeltaNp63alpha) [2.53E-04]	1571	2.79E-03	chr6:127,040,762-127,040,772	11	AGGCAAGGTGG	CCACCTTGCCT