AFF2 (ALF transcription elongation factor 2) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: AFF2 (ALF transcription elongation factor 2) Sus scrofa
Analyze
Symbol: AFF2
Name: ALF transcription elongation factor 2
RGD ID: 14267521
Description: ENCODES a protein that exhibits G-quadruplex RNA binding (inferred); INVOLVED IN learning or memory (ortholog); negative regulation of gene expression (ortholog); nuclear speck organization (ortholog); ASSOCIATED WITH autistic disorder (ortholog); autosomal hemophilia A (ortholog); Dwarfism (ortholog); FOUND IN nuclear speck (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: AF4/FMR2 family member 2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
9097 total Variants

Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
10 2 23 3 2 5 12 10 23 3 6 3

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005654300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984031 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984036 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013984046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_021080471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_021080472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AEMK02000122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CU210920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CU463978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CU606923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CU915474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GFLN01108905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSSSCT00000013917   ⟹   ENSSSCP00000013534
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 EnsemblX120,777,734 - 121,263,569 (+)Ensembl
Ensembl Acc Id: ENSSSCT00000041296   ⟹   ENSSSCP00000037434
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 EnsemblX120,777,734 - 121,263,569 (+)Ensembl
Ensembl Acc Id: ENSSSCT00000058646   ⟹   ENSSSCP00000041528
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 EnsemblX120,777,237 - 121,263,574 (+)Ensembl
RefSeq Acc Id: XM_005654300   ⟹   XP_005654357
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984014   ⟹   XP_013839468
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984020   ⟹   XP_013839474
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,837,441 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984028   ⟹   XP_013839482
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984031   ⟹   XP_013839485
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984035   ⟹   XP_013839489
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984036   ⟹   XP_013839490
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984042   ⟹   XP_013839496
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013984046   ⟹   XP_013839500
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,777,559 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021080471   ⟹   XP_020936130
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,933,615 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021080472   ⟹   XP_020936131
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X120,925,243 - 121,263,574 (+)NCBI
Sequence:
RefSeq Acc Id: XP_013839468   ⟸   XM_013984014
- Peptide Label: isoform X1
- UniProtKB: A0A8D1A9C9 (UniProtKB/TrEMBL),   A0A287A0H6 (UniProtKB/TrEMBL),   A0A8D0T4N8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013839482   ⟸   XM_013984028
- Peptide Label: isoform X4
- UniProtKB: A0A8D0T4N8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013839489   ⟸   XM_013984035
- Peptide Label: isoform X7
- UniProtKB: A0A8D1XKR8 (UniProtKB/TrEMBL),   F1RQ49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013839496   ⟸   XM_013984042
- Peptide Label: isoform X9
- UniProtKB: A0A8D1XKR8 (UniProtKB/TrEMBL),   F1RQ49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005654357   ⟸   XM_005654300
- Peptide Label: isoform X2
- UniProtKB: A0A8D0T4N8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013839485   ⟸   XM_013984031
- Peptide Label: isoform X5
- UniProtKB: A0A8D0T4N8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013839490   ⟸   XM_013984036
- Peptide Label: isoform X8
- UniProtKB: A0A8D1XKR8 (UniProtKB/TrEMBL),   F1RQ49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013839500   ⟸   XM_013984046
- Peptide Label: isoform X10
- UniProtKB: F1RQ49 (UniProtKB/TrEMBL),   A0A480K3V4 (UniProtKB/TrEMBL),   A0A8D1XKR8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013839474   ⟸   XM_013984020
- Peptide Label: isoform X3
- UniProtKB: A0A8D0Y3F0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020936131   ⟸   XM_021080472
- Peptide Label: isoform X11
- UniProtKB: A0A8D0Y3F0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020936130   ⟸   XM_021080471
- Peptide Label: isoform X6
- UniProtKB: A0A8D0Y3F0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSSSCP00000041528   ⟸   ENSSSCT00000058646
Ensembl Acc Id: ENSSSCP00000037434   ⟸   ENSSSCT00000041296
Ensembl Acc Id: ENSSSCP00000013534   ⟸   ENSSSCT00000013917
Protein Domains
AF4/FMR2 C-terminal homology


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000012730 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015013709 UniProtKB/TrEMBL
  ENSSSCG00025068242 UniProtKB/TrEMBL
  ENSSSCG00030067894 UniProtKB/TrEMBL
  ENSSSCG00035052443 UniProtKB/TrEMBL
  ENSSSCG00045035193 UniProtKB/TrEMBL
  ENSSSCG00055000559 UniProtKB/TrEMBL
  ENSSSCG00060047599 UniProtKB/TrEMBL
  ENSSSCG00065011737 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000013917 ENTREZGENE
  ENSSSCT00000013917.6 UniProtKB/TrEMBL
  ENSSSCT00000041296 ENTREZGENE
  ENSSSCT00000041296.3 UniProtKB/TrEMBL
  ENSSSCT00015018384.1 UniProtKB/TrEMBL
  ENSSSCT00025093999.1 UniProtKB/TrEMBL
  ENSSSCT00030094941.1 UniProtKB/TrEMBL
  ENSSSCT00030095073.1 UniProtKB/TrEMBL
  ENSSSCT00035069947.1 UniProtKB/TrEMBL
  ENSSSCT00035069953.1 UniProtKB/TrEMBL
  ENSSSCT00045060822.1 UniProtKB/TrEMBL
  ENSSSCT00045060974.1 UniProtKB/TrEMBL
  ENSSSCT00055001077.1 UniProtKB/TrEMBL
  ENSSSCT00055001108.1 UniProtKB/TrEMBL
  ENSSSCT00055001137.1 UniProtKB/TrEMBL
  ENSSSCT00060064631.1 UniProtKB/TrEMBL
  ENSSSCT00060064641.1 UniProtKB/TrEMBL
  ENSSSCT00065015664.1 UniProtKB/TrEMBL
  ENSSSCT00065015672.1 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 AFF2 ENTREZGENE
PANTHER AF4/FMR2 FAMILY MEMBER 2 UniProtKB/TrEMBL
  PTHR10528 UniProtKB/TrEMBL
Pfam AF-4 UniProtKB/TrEMBL
  AF-4_C UniProtKB/TrEMBL
  AF4_int UniProtKB/TrEMBL
UniProt A0A287A0H6 ENTREZGENE, UniProtKB/TrEMBL
  A0A480K3V4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0T4N8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0Y3F0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1A9C9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1P8Z2_PIG UniProtKB/TrEMBL
  A0A8D1PAT9_PIG UniProtKB/TrEMBL
  A0A8D1VQ50_PIG UniProtKB/TrEMBL
  A0A8D1XKR8 ENTREZGENE, UniProtKB/TrEMBL
  F1RQ49 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:85168 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-20 AFF2  ALF transcription elongation factor 2  AFF2  AF4/FMR2 family member 2  Symbol and/or name change 19259463 PROVISIONAL