Snhg11 Gene Detail

Summary

• Symbol
  Snhg11
• Name
  small nucleolar RNA host gene 11
• Synonyms
  A930034L06Rik, E130013N09Rik

• Feature Type
  protein coding gene
  BioType Conflict
  
• IDs
  MGI:2441845
  NCBI Gene: 319317
• Alliance
  gene page
• Transcription Start Sites
  24 TSS

Location &
Maps

• Sequence Map
  Chr2:158217558-158228071 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 2, 78.72 cM
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  442 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2441845	protein coding gene	Chr2:158217558-158228394 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0026793	protein coding gene	Chr2:163449364-163459861 (+)
A/J	MGP_AJ_G0026759	protein coding gene	Chr2:156890613-156901125 (+)
AKR/J	MGP_AKRJ_G0026730	protein coding gene	Chr2:161514948-161525437 (+)
BALB/cJ	MGP_BALBcJ_G0026768	protein coding gene	Chr2:157195556-157206404 (+)
C3H/HeJ	MGP_C3HHeJ_G0026510	protein coding gene	Chr2:161844647-161855158 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0027217	protein coding gene	Chr2:168324554-168335061 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024587	protein coding gene	Chr2:150332560-150343255 (+)
CAST/EiJ	MGP_CASTEiJ_G0025972	protein coding gene	Chr2:162209137-162219502 (+)
CBA/J	MGP_CBAJ_G0026487	protein coding gene	Chr2:174351856-174362364 (+)
DBA/2J	MGP_DBA2J_G0026625	protein coding gene	Chr2:156065547-156076204 (+)
FVB/NJ	MGP_FVBNJ_G0026592	protein coding gene	Chr2:154475324-154485841 (+)
LP/J	MGP_LPJ_G0026728	protein coding gene	Chr2:163539123-163549614 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026613	protein coding gene	Chr2:178147229-178159166 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027273	protein coding gene	Chr2:161345115-161356770 (+)
PWK/PhJ	MGP_PWKPhJ_G0025706	protein coding gene	Chr2:155600507-155611098 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0025509	protein coding gene	Chr2:160262423-160276728 (+)
WSB/EiJ	MGP_WSBEiJ_G0026042	protein coding gene	Chr2:162238873-162249282 (+)

Homology

• Human Ortholog
  SNHG11, small nucleolar RNA host gene 11

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  SNHG11, small nucleolar RNA host gene 11
  
• Synonyms
  C20orf198, LINC00101, NCRNA00101
• Links
  HGNC:25046

  NCBI Gene ID: 128439

  
  
• Chr Location
  20q11.23; chr20:38446343-38450940 (+)  GRCh38

---

• MGI Vertebrate Homology
  Snhg11 stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: SNHG11
• Gene Tree
  Snhg11
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  3 phenotype references
  

• All Mutations and Alleles
  3
• Targeted
  3
• Find Mice (IMSR)
  7 strains or lines available

Gene Ontology
(GO)
Classifications

Expression

• Assay Results
  1179
• Tissues
  70
• cDNA Data
  20
• Literature Summary
  5

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GENSAT
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  54
• RefSeq
  1
• UniProt
  2
• CCDS
  CCDS38308.1

• Ensembl
  ENSMUSG00000044349 (Evidence)
• NCBI Gene
  319317

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000044349	Ensembl Gene Model | MGI Sequence Detail	10514	C57BL/6J
transcript	ENSMUST00000109488	Ensembl | MGI Sequence Detail	5864	Not Applicable
polypeptide	ENSMUSP00000105114	Ensembl | MGI Sequence Detail	87	Not Applicable

Protein
Information

• UniProt
  2 Sequences

Molecular
Reagents

• All nucleic 22

  cDNA 22

  
  

  Microarray probesets 6

Other
Accession IDs

MGI:2139102, MGI:2139119, MGI:2139341

References

• Summaries
  All 30

  Developmental Gene Expression 5

  Phenotypes 3
• Earliest
  J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
• Latest
  J:351599 Sierra C, et al., The lncRNA Snhg11, a new candidate contributing to neurogenesis, plasticity, and memory deficits in Down syndrome. Mol Psychiatry. 2024 Feb 27;

TSS for Snhg11:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr21315	Chr2:158217623-158217641 (+)	74 bp
Tssr21316	Chr2:158218175-158218215 (+)	637 bp
Tssr21317	Chr2:158223297-158223318 (+)	5,750 bp
Tssr21318	Chr2:158224090-158224094 (+)	6,534 bp
Tssr21319	Chr2:158224489-158224508 (+)	6,941 bp
Tssr21320	Chr2:158224528-158224544 (+)	6,978 bp
Tssr21321	Chr2:158224620-158224654 (+)	7,079 bp
Tssr21322	Chr2:158224765-158224777 (+)	7,213 bp
Tssr21323	Chr2:158224812-158224821 (+)	7,259 bp
Tssr21324	Chr2:158224844-158224859 (+)	7,294 bp
Tssr21325	Chr2:158224884-158224895 (+)	7,332 bp
Tssr21326	Chr2:158224906-158224919 (+)	7,355 bp
Tssr21327	Chr2:158224955-158224956 (+)	7,398 bp
Tssr21328	Chr2:158224993-158225002 (+)	7,440 bp
Tssr21329	Chr2:158225006-158225015 (+)	7,453 bp
Tssr21330	Chr2:158225028-158225104 (+)	7,508 bp
Tssr21331	Chr2:158225601-158225614 (+)	8,050 bp
Tssr21332	Chr2:158225738-158225749 (+)	8,186 bp
Tssr21333	Chr2:158225770-158225779 (+)	8,217 bp
Tssr21334	Chr2:158226537-158226549 (+)	8,985 bp
Tssr21335	Chr2:158226893-158226913 (+)	9,345 bp
Tssr21336	Chr2:158226947-158226949 (+)	9,390 bp
Tssr21337	Chr2:158227051-158227064 (+)	9,500 bp
Tssr21338	Chr2:158227618-158227637 (+)	10,070 bp