HAPLN3 (hyaluronan and proteoglycan link protein 3) - Rat Genome Database

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Gene: HAPLN3 (hyaluronan and proteoglycan link protein 3) Sus scrofa
Analyze
Symbol: HAPLN3
Name: hyaluronan and proteoglycan link protein 3
RGD ID: 14010229
Description: ENCODES a protein that exhibits hyaluronic acid binding (inferred); INVOLVED IN cell adhesion (inferred); central nervous system development (inferred); glial cell differentiation (inferred); ASSOCIATED WITH Bloom syndrome (ortholog); colorectal cancer (ortholog); D-2-hydroxyglutaric aciduria 2 (ortholog); FOUND IN extracellular space (inferred); membrane (inferred); perineuronal net (inferred)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl754,519,800 - 54,537,434 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1754,519,790 - 54,537,429 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2759,486,447 - 59,502,356 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
extracellular space  (IBA,IEA)
membrane  (IEA)
perineuronal net  (IBA,IEA)
synapse  (IBA,IEA)

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
HAPLN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl754,519,800 - 54,537,434 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1754,519,790 - 54,537,429 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2759,486,447 - 59,502,356 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HAPLN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381588,877,294 - 88,895,544 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1588,877,294 - 88,895,597 (-)EnsemblGRCh38hg38GRCh38
GRCh371589,420,525 - 89,438,775 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361587,221,523 - 87,239,774 (-)NCBINCBI36Build 36hg18NCBI36
Build 341587,221,522 - 87,239,774NCBI
Celera1565,821,836 - 65,840,086 (-)NCBICelera
Cytogenetic Map15q26.1NCBI
HuRef1565,532,521 - 65,550,982 (-)NCBIHuRef
CHM1_11589,261,164 - 89,279,411 (-)NCBICHM1_1
T2T-CHM13v2.01586,631,937 - 86,650,187 (-)NCBIT2T-CHM13v2.0
Hapln3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39778,766,775 - 78,783,100 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl778,764,850 - 78,780,766 (-)EnsemblGRCm39 Ensembl
GRCm38779,117,027 - 79,133,173 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl779,115,102 - 79,131,018 (-)EnsemblGRCm38mm10GRCm38
MGSCv37786,261,913 - 86,275,904 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36778,990,540 - 79,004,531 (-)NCBIMGSCv36mm8
Celera776,516,725 - 76,530,397 (-)NCBICelera
Cytogenetic Map7D2NCBI
cM Map744.9NCBI
Hapln3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81142,455,828 - 142,473,877 (-)NCBIGRCr8
mRatBN7.21133,046,465 - 133,064,665 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1133,046,467 - 133,080,177 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1140,963,124 - 140,971,002 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01148,132,553 - 148,140,431 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01141,050,237 - 141,058,112 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01140,827,279 - 140,845,386 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1140,827,295 - 140,835,151 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01141,796,040 - 141,814,155 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41134,851,830 - 134,859,702 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11134,930,188 - 134,938,045 (-)NCBI
Celera1125,117,287 - 125,125,159 (-)NCBICelera
Cytogenetic Map1q31NCBI
Hapln3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541616,105,772 - 16,122,139 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541616,105,937 - 16,122,114 (+)NCBIChiLan1.0ChiLan1.0
HAPLN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21678,421,619 - 78,441,617 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11582,126,180 - 82,145,644 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01567,565,957 - 67,584,352 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11586,773,882 - 86,792,120 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1586,773,882 - 86,792,120 (-)Ensemblpanpan1.1panPan2
HAPLN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1352,033,985 - 52,052,572 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl352,033,991 - 52,051,617 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha354,670,357 - 54,687,625 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0352,452,939 - 52,470,195 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl352,452,939 - 52,499,723 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1351,975,441 - 51,992,700 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0352,185,842 - 52,203,160 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0352,524,684 - 52,541,966 (-)NCBIUU_Cfam_GSD_1.0
Hapln3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640131,466,499 - 131,485,296 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648314,849,183 - 14,859,212 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648314,849,778 - 14,868,094 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HAPLN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1297,419,345 - 7,456,484 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl297,419,329 - 7,439,666 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605939,397,832 - 39,421,309 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hapln3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476816,158,506 - 16,170,558 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476816,146,374 - 16,170,598 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in HAPLN3
405 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 hemolymphoid system nervous system renal system reproductive system respiratory system
High
Medium
Low 3 4 4 2 2 1
Below cutoff 6 1 9 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000023723   ⟹   ENSSSCP00000024189
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl754,519,800 - 54,537,434 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000054334   ⟹   ENSSSCP00000037819
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl754,519,796 - 54,537,753 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000078020   ⟹   ENSSSCP00000073060
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl754,519,698 - 54,537,434 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000087928   ⟹   ENSSSCP00000064934
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl754,519,800 - 54,537,373 (-)Ensembl
RefSeq Acc Id: XM_001925622   ⟹   XP_001925657
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1754,519,790 - 54,537,429 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005653519   ⟹   XP_005653576
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1754,519,790 - 54,537,381 (-)NCBI
Sequence:
RefSeq Acc Id: XM_013996976   ⟹   XP_013852430
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1754,519,790 - 54,537,409 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_001925657   ⟸   XM_001925622
- Peptide Label: isoform X1
- UniProtKB: A0A4X1U6R5 (UniProtKB/TrEMBL),   A0A5G2R305 (UniProtKB/TrEMBL),   A0A8D1BJW7 (UniProtKB/TrEMBL),   A0A8D0JTV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013852430   ⟸   XM_013996976
- Peptide Label: isoform X3
- UniProtKB: I3LJC9 (UniProtKB/TrEMBL),   A0A4X1U6Q5 (UniProtKB/TrEMBL),   A0A8D1WW91 (UniProtKB/TrEMBL),   A0A8D0V1P7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005653576   ⟸   XM_005653519
- Peptide Label: isoform X2
- UniProtKB: A0A8D1BJW7 (UniProtKB/TrEMBL),   A0A8D0JTV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000037819   ⟸   ENSSSCT00000054334
RefSeq Acc Id: ENSSSCP00000073060   ⟸   ENSSSCT00000078020
RefSeq Acc Id: ENSSSCP00000064934   ⟸   ENSSSCT00000087928
RefSeq Acc Id: ENSSSCP00000024189   ⟸   ENSSSCT00000023723
Protein Domains
Ig-like   Link


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000030597 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005028933 UniProtKB/TrEMBL
  ENSSSCG00015040118 UniProtKB/TrEMBL
  ENSSSCG00025075027 UniProtKB/TrEMBL
  ENSSSCG00030024024 UniProtKB/TrEMBL
  ENSSSCG00035080069 UniProtKB/TrEMBL
  ENSSSCG00040069273 UniProtKB/TrEMBL
  ENSSSCG00045039056 UniProtKB/TrEMBL
  ENSSSCG00050033031 UniProtKB/TrEMBL
  ENSSSCG00055007739 UniProtKB/TrEMBL
  ENSSSCG00060076252 UniProtKB/TrEMBL
  ENSSSCG00065042738 UniProtKB/TrEMBL
  ENSSSCG00070014406 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000023723 ENTREZGENE
  ENSSSCT00000023723.4 UniProtKB/TrEMBL
  ENSSSCT00000087928 ENTREZGENE
  ENSSSCT00000087928.2 UniProtKB/TrEMBL
  ENSSSCT00005045909.1 UniProtKB/TrEMBL
  ENSSSCT00005045936.1 UniProtKB/TrEMBL
  ENSSSCT00005045965.1 UniProtKB/TrEMBL
  ENSSSCT00015053427.1 UniProtKB/TrEMBL
  ENSSSCT00015053637.1 UniProtKB/TrEMBL
  ENSSSCT00015053795.1 UniProtKB/TrEMBL
  ENSSSCT00025103442.1 UniProtKB/TrEMBL
  ENSSSCT00025103504.1 UniProtKB/TrEMBL
  ENSSSCT00025103563.1 UniProtKB/TrEMBL
  ENSSSCT00030033408.1 UniProtKB/TrEMBL
  ENSSSCT00030033423.1 UniProtKB/TrEMBL
  ENSSSCT00030033445.1 UniProtKB/TrEMBL
  ENSSSCT00035109560.1 UniProtKB/TrEMBL
  ENSSSCT00035109586.1 UniProtKB/TrEMBL
  ENSSSCT00035109614.1 UniProtKB/TrEMBL
  ENSSSCT00035109623.1 UniProtKB/TrEMBL
  ENSSSCT00040094855.1 UniProtKB/TrEMBL
  ENSSSCT00040094924.1 UniProtKB/TrEMBL
  ENSSSCT00040095021.1 UniProtKB/TrEMBL
  ENSSSCT00045067895.1 UniProtKB/TrEMBL
  ENSSSCT00045067907.1 UniProtKB/TrEMBL
  ENSSSCT00045067930.1 UniProtKB/TrEMBL
  ENSSSCT00050044314.1 UniProtKB/TrEMBL
  ENSSSCT00055015122.1 UniProtKB/TrEMBL
  ENSSSCT00055015168.1 UniProtKB/TrEMBL
  ENSSSCT00055015208.1 UniProtKB/TrEMBL
  ENSSSCT00060104607.1 UniProtKB/TrEMBL
  ENSSSCT00065058435.1 UniProtKB/TrEMBL
  ENSSSCT00065058440.1 UniProtKB/TrEMBL
  ENSSSCT00065058443.1 UniProtKB/TrEMBL
  ENSSSCT00070028252.1 UniProtKB/TrEMBL
  ENSSSCT00070028264.1 UniProtKB/TrEMBL
  ENSSSCT00070028278.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin-like/link_sf UniProtKB/TrEMBL
  CTDL_fold UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  Link_dom UniProtKB/TrEMBL
KEGG Report ssc:100157078 UniProtKB/TrEMBL
NCBI Gene HAPLN3 ENTREZGENE
PANTHER AGGRECAN/VERSICAN PROTEOGLYCAN UniProtKB/TrEMBL
  HYALURONAN AND PROTEOGLYCAN LINK PROTEIN 3 UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
  Xlink UniProtKB/TrEMBL
PRINTS LINKMODULE UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  LINK_1 UniProtKB/TrEMBL
  LINK_2 UniProtKB/TrEMBL
SMART IGv UniProtKB/TrEMBL
  LINK UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
  SSF56436 UniProtKB/TrEMBL
UniProt A0A4X1U1H7_PIG UniProtKB/TrEMBL
  A0A4X1U6Q5 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1U6R5 ENTREZGENE, UniProtKB/TrEMBL
  A0A5G2R305 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0JTV3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0V1P7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1BJW7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1BRH9_PIG UniProtKB/TrEMBL
  A0A8D1PVG1_PIG UniProtKB/TrEMBL
  A0A8D1WW91 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1Z0U7_PIG UniProtKB/TrEMBL
  I3LJC9 ENTREZGENE
UniProt Secondary I3LJC9 UniProtKB/TrEMBL
VGNC ID VGNC:88782 ENTREZGENE