Aff4 (ALF transcription elongation factor 4) - Rat Genome Database

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Gene: Aff4 (ALF transcription elongation factor 4) Rattus norvegicus
Analyze
Symbol: Aff4
Name: ALF transcription elongation factor 4 (Ensembl:AF4/FMR2 family, member 4)
RGD ID: 1311694
Description: Involved in response to endoplasmic reticulum stress. Predicted to be located in euchromatin; fibrillar center; and nucleoplasm. Predicted to be part of super elongation complex. Orthologous to human AFF4 (ALF transcription elongation factor 4); PARTICIPATES IN RNA polymerase II transcription elongation pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: AF4/FMR2 family member 4; AF4/FMR2 family, member 4; Laf4l; LOC303132; lymphoid nuclear protein related to AF4-like
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
mRatBN7.21037,498,825 - 37,579,751 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1037,498,825 - 37,579,751 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1042,191,881 - 42,272,554 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01041,681,915 - 41,762,603 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01037,185,635 - 37,266,323 (+)NCBIRnor_WKY
Rnor_6.01038,692,167 - 38,773,021 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1038,692,211 - 38,773,021 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01038,473,786 - 38,555,300 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41038,798,873 - 38,883,154 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11038,805,468 - 38,883,565 (+)NCBI
Celera1036,846,104 - 36,927,272 (+)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
17beta-estradiol  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
C60 fullerene  (EXP)
caffeine  (ISO)
CGP 52608  (ISO)
chloroprene  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
Enterolactone  (ISO)
ethyl methanesulfonate  (ISO)
fenthion  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
geldanamycin  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
mercury dichloride  (ISO)
methapyrilene  (EXP)
methidathion  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
parathion  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
resveratrol  (EXP,ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
theophylline  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. AFF4 Predicts the Prognosis of Colorectal Cancer Patients and Suppresses Colorectal Cancer Metastasis via Promoting CDH1 Expression. Fang Y, etal., Front Oncol. 2022 Feb 9;12:797392. doi: 10.3389/fonc.2022.797392. eCollection 2022.
2. 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.
3. AFF4 facilitates melanoma cell progression by regulating c-Jun activity. Hu H, etal., Exp Cell Res. 2021 Feb 15;399(2):112445. doi: 10.1016/j.yexcr.2020.112445. Epub 2021 Jan 5.
4. Genipin attenuates mitochondrial-dependent apoptosis, endoplasmic reticulum stress, and inflammation via the PI3K/AKT pathway in acute lung injury. Luo X, etal., Int Immunopharmacol. 2019 Nov;76:105842. doi: 10.1016/j.intimp.2019.105842. Epub 2019 Aug 26.
5. The super elongation complex (SEC) family in transcriptional control. Luo Z, etal., Nat Rev Mol Cell Biol. 2012 Sep;13(9):543-7. doi: 10.1038/nrm3417. Epub 2012 Aug 16.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:16024815   PMID:22195968  


Genomics

Comparative Map Data
Aff4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21037,498,825 - 37,579,751 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1037,498,825 - 37,579,751 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1042,191,881 - 42,272,554 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01041,681,915 - 41,762,603 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01037,185,635 - 37,266,323 (+)NCBIRnor_WKY
Rnor_6.01038,692,167 - 38,773,021 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1038,692,211 - 38,773,021 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01038,473,786 - 38,555,300 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41038,798,873 - 38,883,154 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11038,805,468 - 38,883,565 (+)NCBI
Celera1036,846,104 - 36,927,272 (+)NCBICelera
Cytogenetic Map10q22NCBI
AFF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385132,875,395 - 132,963,634 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl5132,875,395 - 132,963,634 (-)EnsemblGRCh38hg38GRCh38
GRCh375132,211,087 - 132,299,326 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365132,238,970 - 132,327,253 (-)NCBINCBI36Build 36hg18NCBI36
Celera5128,341,097 - 128,429,374 (-)NCBICelera
Cytogenetic Map5q31.1NCBI
HuRef5127,403,706 - 127,491,391 (-)NCBIHuRef
CHM1_15131,644,358 - 131,732,653 (-)NCBICHM1_1
T2T-CHM13v2.05133,395,153 - 133,483,382 (-)NCBIT2T-CHM13v2.0
Aff4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391153,240,807 - 53,312,657 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1153,241,660 - 53,312,657 (+)EnsemblGRCm39 Ensembl
GRCm381153,350,640 - 53,421,830 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1153,350,833 - 53,421,830 (+)EnsemblGRCm38mm10GRCm38
MGSCv371153,164,269 - 53,235,332 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361153,194,256 - 53,265,263 (+)NCBIMGSCv36mm8
Celera1157,930,485 - 58,001,550 (+)NCBICelera
Cytogenetic Map11B1.3NCBI
Aff4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554084,248,563 - 4,305,194 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554084,247,730 - 4,305,194 (-)NCBIChiLan1.0ChiLan1.0
AFF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15134,451,740 - 134,532,517 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5134,457,398 - 134,532,625 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05128,292,700 - 128,374,511 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
AFF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11121,157,790 - 21,218,750 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1121,163,398 - 21,218,190 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1119,960,642 - 20,053,417 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01121,945,075 - 22,033,184 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1121,947,331 - 22,033,241 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11120,663,430 - 20,751,443 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01120,511,144 - 20,599,256 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01121,153,663 - 21,241,674 (-)NCBIUU_Cfam_GSD_1.0
Aff4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213115,239,719 - 115,339,647 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366472,242,319 - 2,336,532 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366472,242,476 - 2,342,409 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AFF4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2135,200,076 - 135,283,675 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12135,196,067 - 135,283,931 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22140,668,525 - 140,696,941 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AFF4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12335,693,427 - 35,782,746 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2335,699,094 - 35,782,683 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603442,158,934 - 42,249,046 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Aff4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473339,123,575 - 39,221,424 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473339,126,483 - 39,226,969 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Aff4
242 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:899
Count of miRNA genes:325
Interacting mature miRNAs:453
Transcripts:ENSRNOT00000009440
Prediction methods:Miranda, Targetscan
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
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat

Markers in Region
SGC32016  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21037,578,868 - 37,579,002 (+)MAPPERmRatBN7.2
Rnor_6.01038,772,139 - 38,772,272NCBIRnor6.0
Rnor_5.01038,554,418 - 38,554,551UniSTSRnor5.0
RGSC_v3.41038,882,272 - 38,882,405UniSTSRGSC3.4
Celera1036,926,390 - 36,926,523UniSTS
Cytogenetic Map10q22UniSTS
RH142595  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21037,573,390 - 37,573,508 (+)MAPPERmRatBN7.2
Rnor_6.01038,766,661 - 38,766,778NCBIRnor6.0
Rnor_5.01038,548,940 - 38,549,057UniSTSRnor5.0
RGSC_v3.41038,876,794 - 38,876,911UniSTSRGSC3.4
Celera1036,920,911 - 36,921,028UniSTS
RH 3.4 Map10402.5UniSTS
Cytogenetic Map10q22UniSTS
AU047273  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21037,569,393 - 37,569,548 (+)MAPPERmRatBN7.2
Rnor_6.01038,762,662 - 38,762,818NCBIRnor6.0
Rnor_5.01038,544,557 - 38,544,713UniSTSRnor5.0
RGSC_v3.41038,872,795 - 38,872,951UniSTSRGSC3.4
Celera1036,916,912 - 36,917,068UniSTS
Cytogenetic Map10q22UniSTS
stSG601610  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21037,552,129 - 37,553,740 (+)MAPPERmRatBN7.2
Rnor_6.01038,745,401 - 38,747,011NCBIRnor6.0
Rnor_5.01038,527,155 - 38,528,765UniSTSRnor5.0
RGSC_v3.41038,854,988 - 38,856,598UniSTSRGSC3.4
Celera1036,899,569 - 36,901,181UniSTS
Cytogenetic Map10q22UniSTS
MARC_16763-16764:1020874272:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21037,523,517 - 37,524,011 (+)MAPPERmRatBN7.2
Rnor_6.01038,716,720 - 38,717,213NCBIRnor6.0
Rnor_5.01038,498,582 - 38,499,075UniSTSRnor5.0
RGSC_v3.41038,824,744 - 38,825,237UniSTSRGSC3.4
Celera1036,870,605 - 36,871,098UniSTS
Cytogenetic Map10q22UniSTS
REN72054  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21037,578,697 - 37,578,929 (+)MAPPERmRatBN7.2
Rnor_6.01038,771,968 - 38,772,199NCBIRnor6.0
Rnor_5.01038,554,247 - 38,554,478UniSTSRnor5.0
RGSC_v3.41038,882,101 - 38,882,332UniSTSRGSC3.4
Celera1036,926,219 - 36,926,450UniSTS
Cytogenetic Map10q22UniSTS


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 40 38 22 19 22 8 9 74 35 38 11 8
Low 3 19 19 19 2 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009440   ⟹   ENSRNOP00000009440
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1037,498,825 - 37,579,751 (+)Ensembl
Rnor_6.0 Ensembl1038,692,211 - 38,773,021 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114150   ⟹   ENSRNOP00000088228
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1037,498,825 - 37,579,751 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117466   ⟹   ENSRNOP00000086504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1037,498,825 - 37,579,751 (+)Ensembl
RefSeq Acc Id: NM_001107001   ⟹   NP_001100471
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,498,825 - 37,579,751 (+)NCBI
Rnor_6.01038,692,211 - 38,773,021 (+)NCBI
Rnor_5.01038,473,786 - 38,555,300 (+)NCBI
RGSC_v3.41038,798,873 - 38,883,154 (+)RGD
Celera1036,846,104 - 36,927,272 (+)RGD
Sequence:
RefSeq Acc Id: XM_006246263   ⟹   XP_006246325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,498,825 - 37,579,044 (+)NCBI
Rnor_6.01038,692,167 - 38,772,314 (+)NCBI
Rnor_5.01038,473,786 - 38,555,300 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006246264   ⟹   XP_006246326
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,498,998 - 37,579,044 (+)NCBI
Rnor_6.01038,692,232 - 38,772,314 (+)NCBI
Rnor_5.01038,473,786 - 38,555,300 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767684   ⟹   XP_008765906
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,511,407 - 37,579,044 (+)NCBI
Rnor_6.01038,704,315 - 38,772,314 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039085930   ⟹   XP_038941858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,524,117 - 37,579,044 (+)NCBI
RefSeq Acc Id: XM_039085931   ⟹   XP_038941859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,531,847 - 37,579,044 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100471   ⟸   NM_001107001
- UniProtKB: D3ZSX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006246325   ⟸   XM_006246263
- Peptide Label: isoform X1
- UniProtKB: D3ZSX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006246326   ⟸   XM_006246264
- Peptide Label: isoform X2
- UniProtKB: A0A8I6GE44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765906   ⟸   XM_008767684
- Peptide Label: isoform X1
- UniProtKB: D3ZSX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009440   ⟸   ENSRNOT00000009440
RefSeq Acc Id: XP_038941858   ⟸   XM_039085930
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038941859   ⟸   XM_039085931
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000086504   ⟸   ENSRNOT00000117466
RefSeq Acc Id: ENSRNOP00000088228   ⟸   ENSRNOT00000114150
Protein Domains
AF-4_C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZSX2-F1-model_v2 AlphaFold D3ZSX2 1-1150 view protein structure

Transcriptome

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

Promoters
RGD ID:13697174
Promoter ID:EPDNEW_R7699
Type:multiple initiation site
Name:Aff4_1
Description:AF4/FMR2 family, member 4
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_6.01038,692,268 - 38,692,328EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311694 AgrOrtholog
BioCyc Gene G2FUF-25145 BioCyc
Ensembl Genes ENSRNOG00000006965 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009440 ENTREZGENE
  ENSRNOP00000009440.7 UniProtKB/TrEMBL
  ENSRNOP00000086504 ENTREZGENE
  ENSRNOP00000086504.1 UniProtKB/TrEMBL
  ENSRNOP00000088228 ENTREZGENE
  ENSRNOP00000088228.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009440 ENTREZGENE
  ENSRNOT00000009440.7 UniProtKB/TrEMBL
  ENSRNOT00000114150 ENTREZGENE
  ENSRNOT00000114150.1 UniProtKB/TrEMBL
  ENSRNOT00000117466 ENTREZGENE
  ENSRNOT00000117466.1 UniProtKB/TrEMBL
InterPro AF-4 UniProtKB/TrEMBL
  AF4/FMR2_C UniProtKB/TrEMBL
  AF4_int UniProtKB/TrEMBL
KEGG Report rno:303132 UniProtKB/TrEMBL
NCBI Gene 303132 ENTREZGENE
PANTHER AF-4 UniProtKB/TrEMBL
Pfam AF-4_C UniProtKB/TrEMBL
  AF4_int UniProtKB/TrEMBL
PhenoGen Aff4 PhenoGen
UniProt A0A8I6GE44 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GGV9_RAT UniProtKB/TrEMBL
  D3ZSX2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-07-05 Aff4  ALF transcription elongation factor 4  Aff4  AF4/FMR2 family, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Aff4  AF4/FMR2 family, member 4   Aff4_predicted  AF4/FMR2 family, member 4 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Aff4_predicted  AF4/FMR2 family, member 4 (predicted)  Laf4l_predicted  lymphoid nuclear protein related to AF4-like (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Laf4l_predicted  lymphoid nuclear protein related to AF4-like (predicted)      Symbol and Name status set to approved 70820 APPROVED