Aff2 (ALF transcription elongation factor 2) - Rat Genome Database

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Gene: Aff2 (ALF transcription elongation factor 2) Rattus norvegicus
Analyze
Symbol: Aff2
Name: ALF transcription elongation factor 2
RGD ID: 1565592
Description: Predicted to enable G-quadruplex RNA binding activity. Predicted to be involved in regulation of RNA splicing. Predicted to act upstream of or within learning or memory; negative regulation of gene expression; and nuclear speck organization. Predicted to be located in nucleus. Predicted to be active in nuclear speck. Human ortholog(s) of this gene implicated in X-linked intellectual developmental disorder 109. Orthologous to human AFF2 (ALF transcription elongation factor 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AF4/FMR2 family member 2; AF4/FMR2 family, member 2; LOC293922; RGD1565592; similar to FMR2 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X152,972,579 - 153,477,080 (+)NCBIGRCr8
mRatBN7.2X147,928,130 - 148,432,484 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX147,928,407 - 148,429,995 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X153,539,951 - 154,051,022 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX153,539,668 - 154,051,181 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01149,265,910 - 149,777,658 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X155,617,378 - 155,970,597 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1132,967,188 - 133,469,753 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11923441   PMID:19136466   PMID:23562910   PMID:26013685  


Genomics

Comparative Map Data
Aff2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X152,972,579 - 153,477,080 (+)NCBIGRCr8
mRatBN7.2X147,928,130 - 148,432,484 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX147,928,407 - 148,429,995 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X153,539,951 - 154,051,022 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX153,539,668 - 154,051,181 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01149,265,910 - 149,777,658 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X155,617,378 - 155,970,597 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1132,967,188 - 133,469,753 (-)NCBICelera
Cytogenetic MapXq37NCBI
AFF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X148,500,617 - 149,000,663 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX148,500,617 - 149,000,663 (+)EnsemblGRCh38hg38GRCh38
GRCh37X147,582,137 - 148,082,193 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X147,389,831 - 147,889,899 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X147,287,684 - 147,787,753NCBI
CeleraX147,930,060 - 148,430,864 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX136,538,903 - 137,039,310 (+)NCBIHuRef
CHM1_1X147,493,410 - 147,993,320 (+)NCBICHM1_1
T2T-CHM13v2.0X146,765,203 - 147,266,230 (+)NCBIT2T-CHM13v2.0
Aff2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X68,403,796 - 68,915,660 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX68,403,900 - 68,911,643 (+)EnsemblGRCm39 Ensembl
GRCm38X69,360,190 - 69,872,054 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX69,360,294 - 69,868,037 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X66,613,506 - 67,121,212 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X65,620,996 - 66,128,702 (+)NCBIMGSCv36mm8
CeleraX60,388,756 - 60,881,813 (+)NCBICelera
Cytogenetic MapXA7.1- A7.2NCBI
cM MapX35.53NCBI
Aff2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554981,012,555 - 1,492,616 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554981,012,323 - 1,497,031 (+)NCBIChiLan1.0ChiLan1.0
AFF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X147,813,480 - 148,304,494 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X147,817,088 - 148,308,102 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X137,524,106 - 138,015,114 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X147,950,886 - 148,446,235 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX147,951,022 - 148,436,935 (+)Ensemblpanpan1.1panPan2
AFF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X116,849,294 - 117,167,875 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX116,696,401 - 117,164,655 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX102,589,304 - 103,060,400 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X118,755,641 - 119,226,966 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX118,755,125 - 119,224,040 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X115,868,624 - 116,336,571 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X118,079,841 - 118,547,888 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X117,807,028 - 118,275,870 (+)NCBIUU_Cfam_GSD_1.0
Aff2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X114,720,953 - 115,196,008 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936513414,574 - 893,676 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936513414,839 - 893,670 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AFF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX120,777,734 - 121,263,569 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X138,260,802 - 138,747,174 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AFF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X123,192,633 - 123,708,505 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX123,338,134 - 123,704,114 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606560,855,652 - 61,357,769 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Aff2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248831,140,886 - 1,611,330 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248831,140,660 - 1,615,672 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Aff2
541 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:28
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000065537
Prediction methods:Miranda, Rnahybrid, 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
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat

Markers in Region
RH131095  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01965,967,927 - 65,968,109NCBIRnor5.0
Rnor_5.01149,620,644 - 149,620,826NCBIRnor5.0
RGSC_v3.41952,722,313 - 52,722,494UniSTSRGSC3.4
RGSC_v3.4X155,617,504 - 155,617,685UniSTSRGSC3.4
Celera1949,735,858 - 49,736,039UniSTS
Celera1133,317,703 - 133,317,884UniSTS
Cytogenetic Map19q12UniSTS
Cytogenetic MapXq37UniSTS
RH137656  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X148,242,995 - 148,243,132 (-)MAPPERmRatBN7.2
Rnor_6.0X153,726,122 - 153,726,258NCBIRnor6.0
Rnor_5.01149,452,275 - 149,452,411UniSTSRnor5.0
RGSC_v3.4X155,784,990 - 155,785,126UniSTSRGSC3.4
Celera1133,155,050 - 133,155,186UniSTS
Cytogenetic MapXq37UniSTS
AU049694  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X148,249,636 - 148,249,791 (-)MAPPERmRatBN7.2
Rnor_6.0X153,719,463 - 153,719,617NCBIRnor6.0
Rnor_5.01149,445,616 - 149,445,770UniSTSRnor5.0
RGSC_v3.4X155,791,629 - 155,791,783UniSTSRGSC3.4
Celera1133,148,243 - 133,148,403UniSTS
Cytogenetic MapXq37UniSTS


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 49 2 19
Low 27 16 6 3 6 2 2 25 20 22 10 2
Below cutoff 2 16 37 31 16 31 6 8 12 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000087990   ⟹   ENSRNOP00000072039
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX147,928,407 - 148,429,995 (+)Ensembl
RefSeq Acc Id: NM_001427288   ⟹   NP_001414217
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X152,972,581 - 153,477,080 (+)NCBI
RefSeq Acc Id: XM_006229538   ⟹   XP_006229600
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X152,972,748 - 153,477,080 (+)NCBI
mRatBN7.2X147,928,130 - 148,432,484 (+)NCBI
Rnor_6.0X153,539,951 - 154,051,022 (-)NCBI
Rnor_5.01149,265,910 - 149,777,658 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229539   ⟹   XP_006229601
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X152,972,579 - 153,477,080 (+)NCBI
mRatBN7.2X147,928,130 - 148,432,484 (+)NCBI
Rnor_6.0X153,539,951 - 154,051,022 (-)NCBI
Rnor_5.01149,265,910 - 149,777,658 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602424   ⟹   XP_017457913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X152,972,748 - 153,477,080 (+)NCBI
mRatBN7.2X147,928,130 - 148,432,484 (+)NCBI
Rnor_6.0X153,539,951 - 154,051,022 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100404   ⟹   XP_038956332
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X153,361,344 - 153,477,080 (+)NCBI
mRatBN7.2X148,316,650 - 148,432,484 (+)NCBI
RefSeq Acc Id: XM_039100405   ⟹   XP_038956333
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X153,381,708 - 153,477,080 (+)NCBI
mRatBN7.2X148,337,028 - 148,432,484 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_006229601   ⟸   XM_006229539
- Peptide Label: isoform X3
- UniProtKB: A6KQ91 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229600   ⟸   XM_006229538
- Peptide Label: isoform X2
- UniProtKB: A6KQ91 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457913   ⟸   XM_017602424
- Peptide Label: isoform X1
- UniProtKB: A6KQ91 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038956332   ⟸   XM_039100404
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038956333   ⟸   XM_039100405
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000072039   ⟸   ENSRNOT00000087990
RefSeq Acc Id: NP_001414217   ⟸   NM_001427288
- UniProtKB: A0A0G2K1Y9 (UniProtKB/TrEMBL)
Protein Domains
AF4/FMR2 C-terminal homology

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KA99-F1-model_v2 AlphaFold A0A0G2KA99 1-1281 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565592 AgrOrtholog
BioCyc Gene G2FUF-736 BioCyc
Ensembl Genes ENSRNOG00000052572 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000087990.2 UniProtKB/TrEMBL
Gene3D-CATH 6.10.250.2670 UniProtKB/TrEMBL
InterPro AF4/FMR2_C UniProtKB/TrEMBL
  AF4_int UniProtKB/TrEMBL
  TF_AF4/FMR2 UniProtKB/TrEMBL
NCBI Gene 293922 ENTREZGENE
PANTHER AF-4 UniProtKB/TrEMBL
  AF4/FMR2 FAMILY MEMBER 2 UniProtKB/TrEMBL
Pfam AF-4 UniProtKB/TrEMBL
  AF-4_C UniProtKB/TrEMBL
  AF4_int UniProtKB/TrEMBL
PhenoGen Aff2 PhenoGen
RatGTEx ENSRNOG00000052572 RatGTEx
UniProt A0A0G2K1Y9 ENTREZGENE, UniProtKB/TrEMBL
  A6KQ91 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-07-05 Aff2  ALF transcription elongation factor 2  Aff2  AF4/FMR2 family, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Aff2  AF4/FMR2 family, member 2   Aff2_predicted  AF4/FMR2 family, member 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Aff2_predicted  AF4/FMR2 family, member 2 (predicted)  RGD1565592_predicted  similar to FMR2 protein (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1565592_predicted  similar to FMR2 protein (predicted)  LOC293922  similar to FMR2 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC293922  similar to FMR2 protein      Symbol and Name status set to provisional 70820 PROVISIONAL