Igkv12-47 Pseudogene Detail

Summary

• Symbol
  Igkv12-47
• Name
  immunoglobulin kappa variable 12-47
• Synonyms
  Gm5574

• Feature Type
  pseudogenic gene segment
• IDs
  MGI:3644595
  NCBI Gene: 434037
• Alliance
  gene page
• Transcription Start Sites
  1 TSS

Location &
Maps

• Sequence Map
  Chr6:69727838-69728294 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 6, 31.60 cM
• Mapping Data
  1 experiment

Strain
Comparison

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

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3644595	pseudogenic gene segment	Chr6:69727838-69728315 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0000279	pseudogenic gene segment	Chr6:70042233-70042710 (-)
A/J	MGP_AJ_G0000252	pseudogenic gene segment	Chr6:67258629-67259106 (-)
AKR/J	MGP_AKRJ_G0000253	pseudogenic gene segment	Chr6:69227890-69228367 (-)
BALB/cJ	MGP_BALBcJ_G0000248	pseudogenic gene segment	Chr6:67427368-67427845 (-)
C3H/HeJ	MGP_C3HHeJ_G0000219	pseudogenic gene segment	Chr6:114960470-114960947 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0000370	pseudogenic gene segment	Chr6:71839802-71840279 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0000119	pseudogenic gene segment	Chr6:66733372-66733833 (-)
CAST/EiJ	MGP_CASTEiJ_G0000240	pseudogenic gene segment	Chr6:69244749-69245226 (-)
CBA/J	MGP_CBAJ_G0000238	pseudogenic gene segment	Chr6:74658389-74658866 (-)
DBA/2J	MGP_DBA2J_G0000236	pseudogenic gene segment	Chr6:66731527-66732004 (-)
FVB/NJ	MGP_FVBNJ_G0000241	pseudogenic gene segment	Chr6:66153034-66153511 (-)
LP/J	MGP_LPJ_G0000289	pseudogenic gene segment	Chr6:69904393-69904870 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0000250	pseudogenic gene segment	Chr6:78367495-78367972 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0000346	pseudogenic gene segment	Chr6:69201508-69201985 (-)
PWK/PhJ	MGP_PWKPhJ_G0000206	pseudogenic gene segment	Chr6:65834161-65834638 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0000180	pseudogenic gene segment	Chr6:67894521-67894998 (-)
WSB/EiJ	MGP_WSBEiJ_G0000242	pseudogenic gene segment	Chr6:69481702-69482179 (-)

Homology

• Human Ortholog
  IGKV6-21, immunoglobulin kappa variable 6-21 (non-functional)

• Vertebrate Orthologs
  6

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  IGKV6-21, immunoglobulin kappa variable 6-21 (non-functional)
  
• Synonyms
  A26, IGKV621
• Links
  HGNC:5836

  NCBI Gene ID: 28906

  UniProt: A0A0C4DH24

  
  
• Chr Location
  2p11.2; chr2:89159751-89160366 (-)  GRCh38

---

• Human Ortholog
  IGKV6D-21, immunoglobulin kappa variable 6D-21 (non-functional)
  
• Synonyms
  A10, IGKV6D21
• Links
  HGNC:5837

  NCBI Gene ID: 28870

  UniProt: A0A0A0MT36

  
  
• Chr Location
  2p11.2; chr2:90021567-90022185 (+)  GRCh38

---

• Human Ortholog
  IGKV6D-41, immunoglobulin kappa variable 6D-41 (non-functional)
  
• Synonyms
  A14
• Links
  HGNC:5838

  NCBI Gene ID: 28869

  UniProt: A0A0C4DH26

  
  
• Chr Location
  2p11.2; chr2:90069662-90070240 (+)  GRCh38

---

• MGI Vertebrate Homology
  Igkv12-47 stringent orthology
  3 human;1 mouse;3 zebrafish
  
• HCOP
  vertebrate homology predictions: IGKV6-21, IGKV6D-21, IGKV6D-41
• Gene Tree
  Igkv12-47
  

Expression

• Assay Results
  706

Tissue x Stage Matrix

• Other Mouse Links
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  22
• RefSeq
  1

• Ensembl
  ENSMUSG00000106256 (Evidence)
• NCBI Gene
  434037

Representative Sequences			Length	Strain/Species
genomic	434037	NCBI Gene Model | MGI Sequence Detail	457	C57BL/6J

References

• Summaries
  All 5
• Earliest
  J:164271 Arnhold J, et al., Human myeloperoxidase in innate and acquired immunity. Arch Biochem Biophys. 2010 Aug 1;500(1):92-106

TSS for Igkv12-47:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr61293	Chr6:69728318-69728332 (-)	-31 bp