PALB2 (partner and localizer of BRCA2) - Rat Genome Database

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Gene: PALB2 (partner and localizer of BRCA2) Canis lupus familiaris
Analyze
Symbol: PALB2
Name: partner and localizer of BRCA2
RGD ID: 12427050
Description: ENCODES a protein that exhibits DNA binding (inferred); INVOLVED IN animal organ morphogenesis (ortholog); apoptotic process (ortholog); embryonic organ development (ortholog); PARTICIPATES IN nuclear factor, erythroid 2 like 2 signaling pathway; ASSOCIATED WITH anaplastic ependymoma (ortholog); B-lymphoblastic leukemia/lymphoma with ETV6-RUNX1 (ortholog); basal cell carcinoma (ortholog); FOUND IN DNA repair complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1622,209,711 - 22,237,798 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl622,209,384 - 22,237,745 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha623,776,491 - 23,804,551 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0622,353,561 - 22,380,176 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl622,353,713 - 22,380,121 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1622,156,874 - 22,184,970 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0622,059,465 - 22,087,651 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0622,454,545 - 22,482,727 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202   PMID:31518051  


Genomics

Comparative Map Data
PALB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1622,209,711 - 22,237,798 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl622,209,384 - 22,237,745 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha623,776,491 - 23,804,551 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0622,353,561 - 22,380,176 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl622,353,713 - 22,380,121 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1622,156,874 - 22,184,970 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0622,059,465 - 22,087,651 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0622,454,545 - 22,482,727 (+)NCBIUU_Cfam_GSD_1.0
PALB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381623,603,165 - 23,641,310 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1623,603,160 - 23,641,321 (-)EnsemblGRCh38hg38GRCh38
GRCh371623,614,486 - 23,652,631 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361623,521,984 - 23,560,179 (-)NCBINCBI36Build 36hg18NCBI36
Celera1622,392,663 - 22,430,856 (-)NCBICelera
Cytogenetic Map16p12.2NCBI
HuRef1621,704,596 - 21,742,312 (-)NCBIHuRef
CHM1_11624,626,195 - 24,664,406 (-)NCBICHM1_1
T2T-CHM13v2.01623,878,974 - 23,917,118 (-)NCBIT2T-CHM13v2.0
Palb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397121,706,485 - 121,732,203 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7121,706,485 - 121,732,208 (-)EnsemblGRCm39 Ensembl
GRCm387122,107,262 - 122,132,980 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7122,107,262 - 122,132,985 (-)EnsemblGRCm38mm10GRCm38
MGSCv377129,250,779 - 129,276,460 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367121,898,410 - 121,924,094 (-)NCBIMGSCv36mm8
Celera7121,997,482 - 122,023,184 (-)NCBICelera
Cytogenetic Map7F2NCBI
cM Map765.42NCBI
Palb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81186,096,312 - 186,120,284 (-)NCBIGRCr8
mRatBN7.21176,665,076 - 176,689,053 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1176,665,076 - 176,688,990 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1184,992,979 - 185,016,822 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01192,178,931 - 192,202,778 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01184,862,806 - 184,886,736 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01192,064,586 - 192,088,547 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1192,064,589 - 192,088,520 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01199,127,037 - 199,151,000 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41180,928,710 - 180,952,518 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11181,068,861 - 181,092,509 (-)NCBI
Celera1174,374,846 - 174,398,646 (-)NCBICelera
Cytogenetic Map1q36NCBI
Palb2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554932,147,862 - 2,175,781 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554932,149,053 - 2,175,482 (-)NCBIChiLan1.0ChiLan1.0
PALB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21825,014,158 - 25,051,771 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11629,533,625 - 29,571,237 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01614,470,367 - 14,507,841 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11623,855,535 - 23,892,117 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1623,855,535 - 23,892,117 (-)Ensemblpanpan1.1panPan2
Palb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344120,149,046 - 120,175,487 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365018,246,927 - 8,273,258 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PALB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl322,586,856 - 22,612,834 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1322,586,881 - 22,612,837 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21017,289 - 43,988 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PALB2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1521,322,952 - 21,358,363 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl521,322,975 - 21,358,198 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660688,438,801 - 8,475,516 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Palb2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247828,751,866 - 8,780,884 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247828,752,510 - 8,780,972 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in PALB2
464 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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium
Low 5 4 22 6 6 6 6 12 8 10 6
Below cutoff 1 6

Sequence


RefSeq Acc Id: ENSCAFT00000049192   ⟹   ENSCAFP00000037206
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl622,209,384 - 22,237,745 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845002856   ⟹   ENSCAFP00845002274
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl622,353,713 - 22,380,121 (+)Ensembl
RefSeq Acc Id: XM_038478784   ⟹   XP_038334712
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1622,156,874 - 22,184,970 (+)NCBI
RefSeq Acc Id: XM_038540031   ⟹   XP_038395959
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0622,454,545 - 22,482,727 (+)NCBI
RefSeq Acc Id: XM_038604106   ⟹   XP_038460034
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0622,059,465 - 22,087,651 (+)NCBI
RefSeq Acc Id: XM_038668831   ⟹   XP_038524759
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0622,353,561 - 22,380,176 (+)NCBI
RefSeq Acc Id: XM_845578   ⟹   XP_850671
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1622,209,711 - 22,237,798 (+)NCBI
Dog10K_Boxer_Tasha623,776,491 - 23,804,551 (+)NCBI
Sequence:
RefSeq Acc Id: XP_850671   ⟸   XM_845578
- UniProtKB: A0A5S9I5Z8 (UniProtKB/TrEMBL),   A0A8P0SS42 (UniProtKB/TrEMBL),   A0A8C0LDG6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000037206   ⟸   ENSCAFT00000049192
RefSeq Acc Id: XP_038334712   ⟸   XM_038478784
RefSeq Acc Id: XP_038460034   ⟸   XM_038604106
RefSeq Acc Id: XP_038524759   ⟸   XM_038668831
- UniProtKB: A0A5S9I5Z8 (UniProtKB/TrEMBL),   A0A8P0SS42 (UniProtKB/TrEMBL),   A0A8C0LDG6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038395959   ⟸   XM_038540031
- UniProtKB: A0A8C0LDG6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845002274   ⟸   ENSCAFT00845002856
Promoters
RGD ID:13683655
Promoter ID:EPDNEW_C1723
Type:single initiation site
Name:PALB2_1
Description:partner and localizer of BRCA2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1622,209,755 - 22,209,815EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000030772 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030020559 UniProtKB/TrEMBL
  ENSCAFG00040003287 UniProtKB/TrEMBL
  ENSCAFG00845001625 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000049192.3 UniProtKB/TrEMBL
  ENSCAFT00030037718.1 UniProtKB/TrEMBL
  ENSCAFT00040006246.1 UniProtKB/TrEMBL
  ENSCAFT00040006272.1 UniProtKB/TrEMBL
  ENSCAFT00040006296.1 UniProtKB/TrEMBL
  ENSCAFT00845002856 ENTREZGENE
  ENSCAFT00845002856.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
InterPro PALB2 UniProtKB/TrEMBL
  PALB2_WD40 UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report cfa:608527 UniProtKB/TrEMBL
NCBI Gene PALB2 ENTREZGENE
PANTHER PARTNER AND LOCALIZER OF BRCA2 UniProtKB/TrEMBL
  PTHR14662 UniProtKB/TrEMBL
Pfam PALB2_WD40 UniProtKB/TrEMBL
Superfamily-SCOP SSF50978 UniProtKB/TrEMBL
UniProt A0A5S9I5Z8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0LDG6 ENTREZGENE
  A0A8C0NVH9_CANLF UniProtKB/TrEMBL
  A0A8C0PXD5_CANLF UniProtKB/TrEMBL
  A0A8C0Q5J0_CANLF UniProtKB/TrEMBL
  A0A8C0QD17_CANLF UniProtKB/TrEMBL
  A0A8P0SS42 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:44245 ENTREZGENE