Nelfb (negative elongation factor complex member B) - Rat Genome Database

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Pathways
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Gene: Nelfb (negative elongation factor complex member B) Rattus norvegicus
Analyze
Symbol: Nelfb
Name: negative elongation factor complex member B
RGD ID: 1307832
Description: Predicted to be involved in several processes, including negative regulation of stem cell differentiation; negative regulation of transcription elongation by RNA polymerase II; and stem cell differentiation. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of NELF complex. Orthologous to human NELFB (negative elongation factor complex member B); PARTICIPATES IN RNA polymerase II transcription elongation pathway; INTERACTS WITH 17beta-estradiol; 4,4'-sulfonyldiphenol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Cobra1; cofactor of BRCA1; LOC311796; negative elongation factor B; negative elongation factor protein B; RGD1307832; similar to cofactor of BRCA1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,409,045 - 28,425,564 (-)NCBIGRCr8
mRatBN7.238,010,883 - 8,027,403 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,010,888 - 8,027,403 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,115,610 - 11,132,086 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,701,839 - 19,718,315 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,891,682 - 17,908,158 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,414,448 - 2,431,148 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,414,451 - 2,431,148 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,395,734 - 2,412,431 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,360,222 - 3,376,609 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,360,218 - 3,376,563 (-)NCBI
Celera32,837,727 - 2,854,117 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
NELF complex  (IBA,ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Control of transcriptional elongation. Kwak H and Lis JT, Annu Rev Genet. 2013;47:483-508. doi: 10.1146/annurev-genet-110711-155440. Epub 2013 Sep 11.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:12612062   PMID:19340312   PMID:24097989   PMID:24656816   PMID:25773599   PMID:26010750  


Genomics

Comparative Map Data
Nelfb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,409,045 - 28,425,564 (-)NCBIGRCr8
mRatBN7.238,010,883 - 8,027,403 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,010,888 - 8,027,403 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,115,610 - 11,132,086 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,701,839 - 19,718,315 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,891,682 - 17,908,158 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,414,448 - 2,431,148 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,414,451 - 2,431,148 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,395,734 - 2,412,431 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,360,222 - 3,376,609 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,360,218 - 3,376,563 (-)NCBI
Celera32,837,727 - 2,854,117 (-)NCBICelera
Cytogenetic Map3p13NCBI
NELFB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389137,255,327 - 137,273,542 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9137,255,327 - 137,273,542 (+)EnsemblGRCh38hg38GRCh38
GRCh379140,149,779 - 140,167,994 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,269,768 - 139,287,815 (+)NCBINCBI36Build 36hg18NCBI36
Celera9110,665,618 - 110,683,794 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,609,072 - 109,627,292 (+)NCBIHuRef
CHM1_19140,298,493 - 140,316,577 (+)NCBICHM1_1
T2T-CHM13v2.09149,492,996 - 149,511,192 (+)NCBIT2T-CHM13v2.0
Nelfb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,089,724 - 25,101,501 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,089,724 - 25,101,501 (-)EnsemblGRCm39 Ensembl
GRCm38225,199,712 - 25,211,489 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,199,712 - 25,211,489 (-)EnsemblGRCm38mm10GRCm38
MGSCv37225,055,232 - 25,067,009 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,021,726 - 25,033,390 (-)NCBIMGSCv36mm8
Celera224,927,483 - 24,939,264 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.06NCBI
Nelfb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,248,190 - 5,262,044 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,248,190 - 5,261,018 (+)NCBIChiLan1.0ChiLan1.0
NELFB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2112,126,248 - 2,144,680 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan192,128,581 - 2,147,028 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09108,314,535 - 108,333,050 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19137,283,264 - 137,301,751 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,278,964 - 137,301,751 (+)Ensemblpanpan1.1panPan2
NELFB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,411,725 - 48,425,044 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,408,005 - 48,423,308 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,598,208 - 47,608,900 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,273,065 - 49,283,756 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,206,548 - 49,287,069 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,049,494 - 48,060,162 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,348,232 - 48,358,986 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,395,161 - 48,405,870 (-)NCBIUU_Cfam_GSD_1.0
Nelfb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,636,347 - 202,648,327 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669726,658 - 738,848 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936669726,731 - 738,714 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NELFB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21314,117,252 - 314,125,940 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NELFB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112914,384 - 933,921 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660584,373,307 - 4,392,656 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nelfb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760692,735 - 705,328 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624760692,735 - 703,571 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nelfb
51 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:223
Count of miRNA genes:170
Interacting mature miRNAs:177
Transcripts:ENSRNOT00000012978
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat


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 renal system reproductive system respiratory system appendage
High
Medium 3 39 50 34 19 34 1 4 74 35 41 11 1
Low 4 7 7 7 7 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012978   ⟹   ENSRNOP00000012978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,010,888 - 8,027,403 (-)Ensembl
Rnor_6.0 Ensembl32,414,451 - 2,431,148 (-)Ensembl
RefSeq Acc Id: NM_001107817   ⟹   NP_001101287
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,409,045 - 28,425,564 (-)NCBI
mRatBN7.238,010,883 - 8,027,403 (-)NCBI
Rnor_6.032,414,448 - 2,431,148 (-)NCBI
Rnor_5.032,395,734 - 2,412,431 (-)NCBI
RGSC_v3.433,360,222 - 3,376,609 (-)RGD
Celera32,837,727 - 2,854,117 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101287 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93634 (Get FASTA)   NCBI Sequence Viewer  
  EDL93635 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012978
  ENSRNOP00000012978.6
Reference Protein Sequences
RefSeq Acc Id: NP_001101287   ⟸   NM_001107817
- UniProtKB: D4ACV0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012978   ⟸   ENSRNOT00000012978

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACV0-F1-model_v2 AlphaFold D4ACV0 1-580 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691860
Promoter ID:EPDNEW_R2384
Type:initiation region
Name:Nelfb_1
Description:negative elongation factor complex member B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,431,076 - 2,431,136EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307832 AgrOrtholog
BioCyc Gene G2FUF-50481 BioCyc
Ensembl Genes ENSRNOG00000009377 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012978 ENTREZGENE
  ENSRNOT00000012978.6 UniProtKB/TrEMBL
InterPro COBRA1 UniProtKB/TrEMBL
NCBI Gene 311796 ENTREZGENE
PANTHER COBRA1 UniProtKB/TrEMBL
  NEGATIVE ELONGATION FACTOR B UniProtKB/TrEMBL
Pfam COBRA1 UniProtKB/TrEMBL
PhenoGen Nelfb PhenoGen
RatGTEx ENSRNOG00000009377 RatGTEx
UniProt D4ACV0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-02-06 Nelfb  negative elongation factor complex member B  Cobra1  cofactor of BRCA1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Cobra1  cofactor of BRCA1  RGD1307832_predicted  similar to cofactor of BRCA1; negative elongation factor protein B (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307832_predicted  similar to cofactor of BRCA1; negative elongation factor protein B (predicted)  LOC311796_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC311796_predicted  similar to cofactor of BRCA1; negative elongation factor protein B (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL