Ess2 (ess-2 splicing factor homolog) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ess2 (ess-2 splicing factor homolog) Rattus norvegicus
Analyze
Symbol: Ess2
Name: ess-2 splicing factor homolog
RGD ID: 1308218
Description: Predicted to act upstream of or within nervous system development. Predicted to be located in nucleus. Predicted to be part of catalytic step 2 spliceosome. Orthologous to human ESS2 (ess-2 splicing factor homolog); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Dgcr14; DiGeorge syndrome critical region gene 14; DiGeorge syndrome critical region gene 14 homolog; DiGeorge syndrome critical region gene 14 homolog (human); DiGeorge syndrome critical region protein 14; LOC360741; MGC109131; splicing factor ESS-2 homolog
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
mRatBN7.21183,075,893 - 83,085,849 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,075,925 - 83,084,846 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,804,553 - 91,813,458 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01184,465,687 - 84,474,592 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01183,519,302 - 83,528,207 (+)NCBIRnor_WKY
Rnor_6.01187,224,371 - 87,234,329 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,224,421 - 87,233,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,315,951 - 90,325,892 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,064,074 - 85,072,979 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11185,104,670 - 85,113,576 (+)NCBI
Celera1181,851,950 - 81,860,857 (+)NCBICelera
Cytogenetic Map11q23NCBI
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:9499415   PMID:11991638  


Genomics

Comparative Map Data
Ess2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21183,075,893 - 83,085,849 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,075,925 - 83,084,846 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,804,553 - 91,813,458 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01184,465,687 - 84,474,592 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01183,519,302 - 83,528,207 (+)NCBIRnor_WKY
Rnor_6.01187,224,371 - 87,234,329 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,224,421 - 87,233,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,315,951 - 90,325,892 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,064,074 - 85,072,979 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11185,104,670 - 85,113,576 (+)NCBI
Celera1181,851,950 - 81,860,857 (+)NCBICelera
Cytogenetic Map11q23NCBI
ESS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382219,130,279 - 19,144,651 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2219,130,279 - 19,144,684 (-)EnsemblGRCh38hg38GRCh38
GRCh372219,117,792 - 19,132,164 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362217,497,792 - 17,512,190 (-)NCBINCBI36Build 36hg18NCBI36
Build 342217,496,005 - 17,506,716NCBI
Celera222,969,816 - 2,984,136 (-)NCBICelera
Cytogenetic Map22q11.21NCBI
HuRef222,739,334 - 2,753,654 (-)NCBIHuRef
CHM1_12219,117,373 - 19,131,693 (-)NCBICHM1_1
T2T-CHM13v2.02219,504,893 - 19,519,192 (-)NCBIT2T-CHM13v2.0
Ess2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,718,573 - 17,729,225 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1617,718,573 - 17,729,212 (-)EnsemblGRCm39 Ensembl
GRCm381617,900,709 - 17,911,348 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1617,900,709 - 17,911,348 (-)EnsemblGRCm38mm10GRCm38
MGSCv371617,900,802 - 17,911,441 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361617,815,328 - 17,824,904 (-)NCBIMGSCv36mm8
Celera1618,473,774 - 18,484,413 (-)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1611.09NCBI
Ess2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544218,828,976 - 18,840,542 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544218,829,037 - 18,840,542 (+)NCBIChiLan1.0ChiLan1.0
ESS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12217,566,021 - 17,576,686 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2217,566,021 - 17,576,686 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0221,884,790 - 1,899,081 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ESS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12630,037,954 - 30,048,487 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2630,038,015 - 30,049,204 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2629,992,001 - 30,002,526 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02631,439,211 - 31,449,740 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2631,439,263 - 31,451,472 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12629,487,358 - 29,497,896 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02629,111,803 - 29,122,336 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02630,199,961 - 30,210,480 (+)NCBIUU_Cfam_GSD_1.0
Ess2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118139,599,975 - 139,621,834 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366193,130,927 - 3,154,098 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366193,132,234 - 3,154,091 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ESS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1450,945,122 - 50,955,983 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11450,945,121 - 50,956,018 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21454,511,952 - 54,522,954 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ESS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1196,604,275 - 6,615,316 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl196,604,345 - 6,615,055 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666085317,603 - 328,601 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ess2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624945176,678 - 188,040 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624945176,773 - 187,586 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ess2
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:59
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000000308
Prediction methods: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
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
2302043Pia27Pristane induced arthritis QTL 2718.60.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)118256654583440803Rat

Markers in Region
RH137472  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,084,541 - 83,084,743 (+)MAPPERmRatBN7.2
Rnor_6.01187,233,022 - 87,233,223NCBIRnor6.0
Rnor_5.01190,324,585 - 90,324,786UniSTSRnor5.0
RGSC_v3.41185,072,675 - 85,072,876UniSTSRGSC3.4
Celera1181,860,553 - 81,860,754UniSTS
Cytogenetic Map11q23UniSTS
UniSTS:496799  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,076,981 - 83,077,232 (+)MAPPERmRatBN7.2
Rnor_6.01187,225,462 - 87,225,712NCBIRnor6.0
Rnor_5.01190,317,025 - 90,317,275UniSTSRnor5.0
RGSC_v3.41185,065,115 - 85,065,365UniSTSRGSC3.4
Celera1181,852,991 - 81,853,241UniSTS
Cytogenetic Map11q23UniSTS
UniSTS:478969  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,079,195 - 83,079,945 (+)MAPPERmRatBN7.2
Rnor_6.01187,227,676 - 87,228,425NCBIRnor6.0
Rnor_5.01190,319,239 - 90,319,988UniSTSRnor5.0
RGSC_v3.41185,067,329 - 85,068,078UniSTSRGSC3.4
Celera1181,855,207 - 81,855,956UniSTS
Cytogenetic Map11q23UniSTS


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 29 28 18 19 18 2 74 27 41 11
Low 14 29 23 23 8 9 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000308   ⟹   ENSRNOP00000000308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,075,925 - 83,084,846 (+)Ensembl
Rnor_6.0 Ensembl1187,224,421 - 87,233,326 (+)Ensembl
RefSeq Acc Id: NM_001012472   ⟹   NP_001012490
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,075,941 - 83,084,846 (+)NCBI
Rnor_6.01187,224,421 - 87,233,326 (+)NCBI
Rnor_5.01190,315,951 - 90,325,892 (+)NCBI
RGSC_v3.41185,064,074 - 85,072,979 (+)RGD
Celera1181,851,950 - 81,860,857 (+)RGD
Sequence:
RefSeq Acc Id: XM_006248635   ⟹   XP_006248697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,075,918 - 83,085,849 (+)NCBI
Rnor_6.01187,224,372 - 87,234,329 (+)NCBI
Rnor_5.01190,315,951 - 90,325,892 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006248636   ⟹   XP_006248698
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,075,918 - 83,085,849 (+)NCBI
Rnor_6.01187,224,371 - 87,234,329 (+)NCBI
Rnor_5.01190,315,951 - 90,325,892 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088524   ⟹   XP_038944452
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,079,325 - 83,085,849 (+)NCBI
RefSeq Acc Id: XR_005491044
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,075,918 - 83,085,849 (+)NCBI
RefSeq Acc Id: XR_005491045
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,075,893 - 83,081,500 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001012490 (Get FASTA)   NCBI Sequence Viewer  
  XP_006248697 (Get FASTA)   NCBI Sequence Viewer  
  XP_006248698 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944452 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH89898 (Get FASTA)   NCBI Sequence Viewer  
  EDL77911 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001012490   ⟸   NM_001012472
- UniProtKB: Q5EB95 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248698   ⟸   XM_006248636
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006248697   ⟸   XM_006248635
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000000308   ⟸   ENSRNOT00000000308
RefSeq Acc Id: XP_038944452   ⟸   XM_039088524
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5EB95-F1-model_v2 AlphaFold Q5EB95 1-480 view protein structure

Transcriptome

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

Promoters
RGD ID:13698314
Promoter ID:EPDNEW_R8839
Type:initiation region
Name:Ess2_1
Description:ess-2 splicing factor homolog
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_6.01187,224,409 - 87,224,469EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308218 AgrOrtholog
BioCyc Gene G2FUF-20620 BioCyc
Ensembl Genes ENSRNOG00000000283 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000308 ENTREZGENE
  ENSRNOP00000000308.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000308 ENTREZGENE
  ENSRNOT00000000308.5 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7382217 IMAGE-MGC_LOAD
InterPro Nuclear_protein_DGCR14 UniProtKB/TrEMBL
KEGG Report rno:360741 UniProtKB/TrEMBL
MGC_CLONE MGC:109131 IMAGE-MGC_LOAD
NCBI Gene 360741 ENTREZGENE
PANTHER PTHR12940 UniProtKB/TrEMBL
Pfam Es2 UniProtKB/TrEMBL
PhenoGen Ess2 PhenoGen
UniProt F7ESE9_RAT UniProtKB/TrEMBL
  Q5EB95 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-06-12 Ess2  ess-2 splicing factor homolog  Dgcr14  DiGeorge syndrome critical region gene 14  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Dgcr14  DiGeorge syndrome critical region gene 14  Dgcr14  DiGeorge syndrome critical region gene 14  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Dgcr14  DiGeorge syndrome critical region gene 14  Dgcr14  DiGeorge syndrome critical region gene 14 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Dgcr14  DiGeorge syndrome critical region gene 14 homolog (human)    DiGeorge syndrome critical region gene 14  Name updated 1299863 APPROVED
2005-12-06 Dgcr14  DiGeorge syndrome critical region gene 14  Dgcr14_predicted  DiGeorge syndrome critical region gene 14 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Dgcr14_predicted  DiGeorge syndrome critical region gene 14 (predicted)      Symbol and Name status set to approved 70820 APPROVED