Pantr1 Gene Detail

Summary

• Symbol
  Pantr1
• Name
  POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1
• Synonyms
  2610017I09Rik, linc-Brn1a, Pou3f3os

• Feature Type
  lncRNA gene
• IDs
  MGI:1913547
  NCBI Gene: 66297
• Alliance
  genome feature page
• Transcription Start Sites
  13 TSS

Location &
Maps

• Sequence Map
  Chr1:42687360-42733985 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 1, 21.08 cM
• Mapping Data
  1 experiment

Strain
Comparison

• SNPs within 2kb
  1017 from dbSNP Build 142
• Strain Annotations
  30

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1913547	lncRNA gene	Chr1:42629754-42734584 (-)
129S1/SvImJ	ENSMUSG00200003408	protein coding gene	Chr1:40300893-40347242 (-)
129S1/SvImJ	ENSMUSG00200004827	lncRNA gene	Chr1:40242820-40348279 (-)
A/J	ENSMUSG00195044653	lncRNA gene	Chr1:39949950-40054842 (-)
A/J	ENSMUSG00195038846	protein coding gene	Chr1:40007494-40052702 (-)
AKR/J	ENSMUSG00220009753	lncRNA gene	Chr1:39945964-40049123 (-)
AKR/J	ENSMUSG00220008986	protein coding gene	Chr1:40001669-40046963 (-)
BALB/cJ	ENSMUSG00180011577	protein coding gene	Chr1:40028155-40073355 (-)
BALB/cJ	ENSMUSG00180012637	lncRNA gene	Chr1:39970645-40075495 (-)
C3H/HeJ	ENSMUSG00175001030	protein coding gene	Chr1:40015270-40060469 (-)
C3H/HeJ	ENSMUSG00175001609	lncRNA gene	Chr1:39957737-40062609 (-)
C57BL/6NJ	ENSMUSG00215028716	protein coding gene	Chr1:40003240-40048430 (-)
C57BL/6NJ	ENSMUSG00215030639	lncRNA gene	Chr1:39945714-40050570 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0004361	lincRNA gene	Chr1:37136313-37235701 (-)
CAST/EiJ	ENSTCUG00005003101	lncRNA gene	Chr1:40021151-40129782 (-)
CBA/J	ENSMUSG00210006035	lncRNA gene	Chr1:39709303-39814133 (-)
CBA/J	ENSMUSG00210005114	protein coding gene	Chr1:39766815-39811993 (-)
DBA/2J	ENSMUSG00185009901	protein coding gene	Chr1:40867928-40913136 (-)
DBA/2J	ENSMUSG00185011173	lncRNA gene	Chr1:40810399-40915275 (-)
FVB/NJ	ENSMUSG00205037166	lncRNA gene	Chr1:39902950-40007836 (-)
FVB/NJ	ENSMUSG00205020718	protein coding gene	Chr1:39960481-40005694 (-)
JF1/MsJ	no annotation
LP/J	ENSMUSG00230026847	lncRNA gene	Chr1:40856335-40961160 (-)
LP/J	ENSMUSG00230020475	protein coding gene	Chr1:40913892-40959021 (-)
NOD/ShiLtJ	ENSMUSG00190026967	protein coding gene	Chr1:39980317-40025502 (-)
NOD/ShiLtJ	ENSMUSG00190042708	lncRNA gene	Chr1:39922801-40027641 (-)
NZO/HlLtJ	ENSMUSG00225000639	lncRNA gene	Chr1:44093305-44198091 (-)
NZO/HlLtJ	ENSMUSG00225000258	protein coding gene	Chr1:44150837-44195935 (-)
PWK/PhJ	ENSLUMG00010038629	lncRNA gene	Chr1:39551340-39654493 (-)
SPRET/EiJ	ENSMSPG00010013863	lncRNA gene	Chr1:41115883-41226938 (-)
WSB/EiJ	ENSIUOG00005039371	lncRNA gene	Chr1:39858635-39963483 (-)

Homology

• Human Ortholog
  PANTR1, POU3F3 adjacent non-coding transcript 1

• Vertebrate Orthologs
  1

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PANTR1, POU3F3 adjacent non-coding transcript 1
  
• Synonyms
  LINC01114, LINC01158, linc-Brn1a, linc-POU3F3
• Links
  HGNC:49513

  NCBI Gene ID: 100506421

  
  
• Chr Location
  chr2:104656012-104857008 (-)  GRCh38

---

• MGI Vertebrate Homology
  Pantr1 stringent orthology
  1 human;1 mouse
  
• HCOP
  vertebrate homology predictions: PANTR1
• Gene Tree
  Pantr1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  1 phenotype from 1 allele in 1 genetic background
  6 phenotype references
  

• All Mutations and Alleles
  2
• Chemically induced (other)
  1
• Targeted
  1
• Genomic Mutations
  1 involving Pantr1
• Find Mice (IMSR)
  0 strains or lines available

Mice homozygous for a null allele are viable.

Expression

• Assay Results
  620
• Tissues
  22
• cDNA Data
  26
• Literature Summary
  9

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  76
• RefSeq
  1
• UniProt
  1

• Ensembl
  ENSMUSG00000060424 (Evidence)
• NCBI Gene
  66297

Representative Sequences			Length	Strain/Species
genomic	66297	NCBI Gene Model | MGI Sequence Detail	46626	C57BL/6J
transcript	NR_027826	RefSeq | MGI Sequence Detail	546	C57BL/6
polypeptide	Q8BTB3	UniProt | EBI | MGI Sequence Detail	65	Not Applicable

Protein
Information

• UniProt
  1 Sequence

Molecular
Reagents

• All nucleic 29

  cDNA 26

  Primer pair 1

  Other 2

  
  

  Microarray probesets 1

References

• Summaries
  All 25

  Developmental Gene Expression 9

  Phenotypes 6
• Earliest
  J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
• Latest
  J:368627 Gather F, et al., The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1. Nucleic Acids Res. 2025 Jun 20;53(12)

TSS for Pantr1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr11463	Chr1:42734572-42734617 (-)	-610 bp
Tssr11462	Chr1:42734439-42734450 (-)	-460 bp
Tssr11461	Chr1:42734351-42734364 (-)	-373 bp
Tssr11460	Chr1:42734108-42734174 (-)	-156 bp
Tssr11459	Chr1:42733973-42734037 (-)	-20 bp
Tssr11458	Chr1:42732307-42732318 (-)	1,672 bp
Tssr11457	Chr1:42732277-42732297 (-)	1,698 bp
Tssr11456	Chr1:42732260-42732271 (-)	1,719 bp
Tssr11455	Chr1:42720592-42720595 (-)	13,391 bp
Tssr11454	Chr1:42706798-42706833 (-)	27,169 bp
Tssr11453	Chr1:42704236-42704246 (-)	29,744 bp
Tssr11452	Chr1:42693652-42693657 (-)	40,330 bp
Tssr11451	Chr1:42690484-42690488 (-)	43,499 bp