SMTNL1 (smoothelin like 1) - Rat Genome Database

Name: SMTNL1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: SMTNL1 (smoothelin like 1) Sus scrofa

Analyze

Symbol:

SMTNL1

Name:

smoothelin like 1

RGD ID:

14271395

Description:

ENCODES a protein that exhibits calmodulin binding (ortholog); CH domain binding (ortholog); disordered domain specific binding (ortholog); INVOLVED IN muscle organ morphogenesis (ortholog); negative regulation of DNA-templated transcription (ortholog); positive regulation of vasoconstriction (ortholog); ASSOCIATED WITH genetic disease (ortholog); intellectual disability (ortholog); FOUND IN contractile muscle fiber (ortholog); cytoplasm (ortholog); I band (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

smoothelin-like protein 1

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	SMTNL1 (smoothelin like 1)	HGNC	NCBI
Mus musculus (house mouse):	Smtnl1 (smoothelin-like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Smtnl1 (smoothelin-like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Smtnl1 (smoothelin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SMTNL1 (smoothelin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SMTNL1 (smoothelin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Smtnl1 (smoothelin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SMTNL1 (smoothelin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Smtnl1 (smoothelin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	2	13,370,920 - 13,384,843 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

intellectual disability (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

actin cytoskeleton organization (IEA)

muscle organ morphogenesis (ISO)

negative regulation of DNA-templated transcription (ISO)

positive regulation of vasoconstriction (ISO)

response to activity (ISO)

response to xenobiotic stimulus (ISO)

vasoconstriction (ISO)

Cellular Component

contractile muscle fiber (ISO)

cytoplasm (ISO)

filamentous actin (IEA)

I band (ISO)

M band (ISO)

microtubule organizing center (IEA)

nucleus (ISO)

Molecular Function

calmodulin binding (ISO)

CH domain binding (ISO)

disordered domain specific binding (ISO)

protein binding (ISO)

protein phosphatase 1 binding (ISO)

tropomyosin binding (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

SMTNL1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	2	13,370,920 - 13,384,843 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

SMTNL1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	57,537,595 - 57,550,272 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	11	57,537,595 - 57,550,272 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	11	57,305,068 - 57,317,745 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	57,065,555 - 57,074,684 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	11	54,666,633 - 54,674,266 (+)	NCBI		Celera
Cytogenetic Map	11	q12.1	NCBI
HuRef	11	53,658,903 - 53,666,539 (+)	NCBI		HuRef
CHM1_1	11	57,176,354 - 57,183,988 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	11	57,487,765 - 57,500,440 (+)	NCBI		T2T-CHM13v2.0

Smtnl1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	84,641,494 - 84,657,173 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	84,641,520 - 84,652,996 (-)	Ensembl		GRCm39 Ensembl
GRCm38	2	84,811,173 - 84,826,847 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	84,811,176 - 84,822,652 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	84,651,333 - 84,662,809 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	84,612,015 - 84,623,491 (-)	NCBI		MGSCv36	mm8
Celera	2	86,406,709 - 86,421,097 (-)	NCBI		Celera
Cytogenetic Map	2	D	NCBI
cM Map	2	49.45	NCBI

Smtnl1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	90,295,682 - 90,307,769 (-)	NCBI		GRCr8
mRatBN7.2	3	69,889,010 - 69,901,096 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	69,889,010 - 69,901,079 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	73,270,699 - 73,278,699 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	81,869,366 - 81,877,366 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	79,628,355 - 79,636,353 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	72,207,150 - 72,219,209 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	72,207,113 - 72,219,246 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	78,728,182 - 78,740,150 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	68,017,296 - 68,025,299 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	67,913,666 - 67,921,671 (-)	NCBI
Celera	3	69,248,302 - 69,252,187 (-)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI

Smtnl1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955511	2,515,651 - 2,521,077 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955511	2,512,950 - 2,521,200 (+)	NCBI	ChiLan1.0	ChiLan1.0

SMTNL1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	9	58,692,926 - 58,706,659 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	11	59,713,177 - 59,725,017 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	11	52,777,777 - 52,792,165 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	11	56,250,161 - 56,262,842 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	56,255,219 - 56,262,685 (+)	Ensembl	panpan1.1		panPan2

SMTNL1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	18	38,620,810 - 38,632,580 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	38,621,066 - 38,628,762 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	38,166,926 - 38,178,671 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	18	39,302,779 - 39,314,560 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	18	39,303,092 - 39,314,489 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	18	38,885,372 - 38,897,148 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	18	38,459,013 - 38,470,701 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	18	39,089,411 - 39,101,187 (-)	NCBI		UU_Cfam_GSD_1.0

Smtnl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	14,841,247 - 14,851,914 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936581	4,955,071 - 4,965,785 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936581	4,955,072 - 4,965,760 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SMTNL1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	15,682,270 - 15,697,126 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	1	15,679,502 - 15,696,462 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	113,036,406 - 113,044,258 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Smtnl1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624864	3,114,210 - 3,121,831 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in SMTNL1
506 total Variants

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	musculoskeletal system	nervous system	reproductive system
High
Medium		2
Low	1
Below cutoff	2		3	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_021083035	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000007	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01012463	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_021083035 ⟹ XP_020938694

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	2	13,370,920 - 13,384,843 (-)	NCBI

Sequence:

show sequence

GGCGGGGACTGAAGAGCTGGGGGCTAGAAGCCACTGGGGCTGAAAGACAGCCAGGGAGTGAGGC
CGCTCAGCTAGAGGAAGGAGGCAGCTCCAAGCCCCCAGGGCAGAGGCCCGTCAGAGATGGAGCA
GAAGAAAGGGAAGCCCTCTGAGGACGGGACCACTGTCTCCCCAGCCACGGAGGCCCCAGAGACG
GTGGGAGGTGGAGCCTCTGCAGAGGACGAGGCCACAGGCCCAGCTGAGAGGTCTGTCAACGAGG
GGCCTCCAGGTGGGGCAGGAAAGCGGGAGAGTGCACCAGCCAAGGACGACACATCAGCTGAATT
CCAGGGGGAAGCAGATGGGTTGGATGAGGTCAAGGTGGAACCCAAAGGGAAGGCTGAACTTCAA
AAGGAGGATGGTGGGAAGGAAGAGACCGACTCTGAACTCAAGGAGGCTGAGGGAAAAGAGACCA
CATTGGCCTCTGAGAACCAGATGGCTGATGAGAAAGAGGCCAAGCCTGGATCTAGGGAGAAAGC
TAACGTGAATGATGAGGCCAAAGCTGAGCCGAAGCAAGCCACTGACAAGGAGGAGGCCACCACG
GTCTCTCAGGAGGAGAATGACAAGACAGAAGAGCCTAAGGCTGAGGCCCAGGATAAAGCCTGTG
CTCCAGAAGCCAAGTCGGACTCTCAGAAGAAGGCTGCCATGGAAGAGGAGGCCAAGGCTGAACC
GCAGGAGGAGGAAGAGATGAAGGAGGAGCTGGAGCCAGGCAGCCCTGATGAAGAGCAGAACCAG
GGTATGGAGGGAGAGTCAGAGGAAGGCGCAGGAGTGCCTCCCAGCTCCCCGGAGGAGTGGCCAG
AGAGCCCCACGGAGGAGGGCGGCGGCCCCAGCCCAGATGGGCTGAGTCCAATTGCCGAAGCTTC
CGGAGAGACCAGTCCTTCAGCCAGTGAATCCTCGCCCAGCGATGTACCCCAGAGCCCCACAGAG
CCCCCGCCCTCACAGGAGAAGAAGAAGGAAAGGGCACCAGAGCGGAGGGTGTCAGCCCCTGTCC
GGCCCCGGGGGCCCCGGGCCCAGAACCGCAAGGCCATCGTGGACAAGTTTGGCGGGGCAGCCTC
GGGCCCCACCGCCCTGTTCCGGAACACCAAGGCCGCAGGGGCTGCCATCGGCGGTGTTAAGAAC
ATGCTCTTGGAGTGGTGCCGGGCCATGACTAGGAACTACGAGCACGTGGACATCCAGAACTTCT
CCTCCAGCTGGAGCAGCGGCATGGCCTTCTGCGCCCTCATCCACAAGTTCTTCCCCGATGCCTT
TGACTATGCTGAGCTGGACCCCACAAAGCGCAGGCACAACTTCACCTTGGCCTTCTCCACGGCA
GAGAAGCTGGCTGACTGCGCCCAGCTGCTGGAGGTGGATGACATGGTGCGGCTGGCAGTGCCTG
ACTCCAAGTGCGTCTACACCTACATCCAGGAGCTGTACCGCAGCCTCGTGCAAAAGGGGCTGGT
GAAGACCAAGAAGAAATGAGGGGCTGCCGACCTGGTAGGCAGAGCGCCCAGCTGATCAGAGGCT
CACTTCTGCTCCATGGAGGTAGCAGCAGCGCTGGGGCTCAGGCAGGCGCAGATGGCACCAGTTT
TAACCACATTAAAAGTTCTTTTGTAAAATCT

hide sequence

Protein Sequences


Protein RefSeqs	XP_020938694	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSSCP00005004783.1
	ENSSSCP00005004798.1
	ENSSSCP00005004820.1

RefSeq Acc Id:

XP_020938694 ⟸ XM_021083035

- UniProtKB:

A0A8D0HVD2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEQKKGKPSEDGTTVSPATEAPETVGGGASAEDEATGPAERSVNEGPPGGAGKRESAPAKDDTS
AEFQGEADGLDEVKVEPKGKAELQKEDGGKEETDSELKEAEGKETTLASENQMADEKEAKPGSR
EKANVNDEAKAEPKQATDKEEATTVSQEENDKTEEPKAEAQDKACAPEAKSDSQKKAAMEEEAK
AEPQEEEEMKEELEPGSPDEEQNQGMEGESEEGAGVPPSSPEEWPESPTEEGGGPSPDGLSPIA
EASGETSPSASESSPSDVPQSPTEPPPSQEKKKERAPERRVSAPVRPRGPRAQNRKAIVDKFGG
AASGPTALFRNTKAAGAAIGGVKNMLLEWCRAMTRNYEHVDIQNFSSSWSSGMAFCALIHKFFP
DAFDYAELDPTKRRHNFTLAFSTAEKLADCAQLLEVDDMVRLAVPDSKCVYTYIQELYRSLVQK
GLVKTKKK

hide sequence

Protein Domains

Calponin-homology (CH)

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00005005491	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00005008212.1	UniProtKB/TrEMBL
	ENSSSCT00005008233.1	UniProtKB/TrEMBL
	ENSSSCT00005008267.1	UniProtKB/TrEMBL
Gene3D-CATH	Calponin-like domain	UniProtKB/TrEMBL
InterPro	CH_dom	UniProtKB/TrEMBL
	CH_dom_sf	UniProtKB/TrEMBL
NCBI Gene	SMTNL1	ENTREZGENE
PANTHER	CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED	UniProtKB/TrEMBL
	SMOOTHELIN-LIKE PROTEIN 1	UniProtKB/TrEMBL
Pfam	PF00307	UniProtKB/TrEMBL
PROSITE	PS50021	UniProtKB/TrEMBL
SMART	SM00033	UniProtKB/TrEMBL
Superfamily-SCOP	Calponin-homology domain, CH-domain	UniProtKB/TrEMBL
UniProt	A0A8D0HVD2	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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