Tcea1l1 (transcription elongation factor A1-like 1)

Gene: Tcea1l1 (transcription elongation factor A1-like 1) Rattus norvegicus

Analyze

No known orthologs.

Symbol:

Tcea1l1

Name:

transcription elongation factor A1-like 1

RGD ID:

1591965

Description:

Orthologous to human TCEA1 (transcription elongation factor A1).

Type:

pseudo (Ensembl: protein-coding)

RefSeq Status:

INFERRED

Previously known as:

AABR07017110.1; LOC498453; similar to transcription elongation factor A 1 isoform 2; transcription elongation factor A protein 1

RGD Orthologs

Alliance Genes

More Info

homologs ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Other homologs ²				less info ...
Homo sapiens (human):	TCEA1 (transcription elongation factor A1)	HGNC	HomoloGene
Alliance orthologs ³
Homo sapiens (human):	TCEA1 (transcription elongation factor A1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Tcea1 (transcription elongation factor A (SII) 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	tcea1 (transcription elongation factor A (SII), 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	DST1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG8117	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PhylomeDB)
Caenorhabditis elegans (roundworm):	T24H10.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	TfIIS	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	tcea1	Alliance	DIOPT (OMA\|OrthoFinder\|PhylomeDB)

Related Functional Gene:

Tcea1

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	12,831,858 - 12,832,763 (+)	NCBI		GRCr8
mRatBN7.2	15	10,401,141 - 10,402,046 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	10,400,829 - 10,402,942 (+)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	15	11,649,874 - 11,652,109 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	14,511,183 - 14,548,429 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	15,688,613 - 15,690,822 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	11,879,456 - 11,880,993 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	15	10,411,382 - 10,412,915 (+)	NCBI		Celera
Cytogenetic Map	15	p16	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation 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.	GOA pipeline	RGD automated data pipeline
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12761297	PMID:16581793	PMID:27193682

Genomics

Variants

Variants in Tcea1l1
5 total Variants

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1354657	Despr13	Despair related QTL 13		0.0022	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	15	1	29912054	Rat
8552920	Pigfal8	Plasma insulin-like growth factor 1 level QTL 8	3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	15	1	34723002	Rat
8694361	Abfw6	Abdominal fat weight QTL 6	10.2	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	15	1	34723002	Rat
9589149	Insul29	Insulin level QTL 29	9.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	15	1	34723002	Rat
731170	Pur3	Proteinuria QTL 3	2.3	0.0005	urine protein amount (VT:0005160)	urine protein excretion rate (CMO:0000759)	15	1	41686771	Rat
1641887	Alcrsp14	Alcohol response QTL 14			response to alcohol trait (VT:0010489)	brain neurotensin receptor 1 density (CMO:0002068)	15	1	42356671	Rat
2298549	Neuinf12	Neuroinflammation QTL 12	3.5		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	15	1	55302115	Rat
10401805	Kidm51	Kidney mass QTL 51			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	15	306329	45306329	Rat
5684946	Bss98	Bone structure and strength QTL 98	3.9	0.0026	tibia strength trait (VT:1000284)	tibia ultimate force (CMO:0001734)	15	1058250	14481294	Rat
1641913	Colcr2	Colorectal carcinoma resistance QTL 2	6.57	0.0197	intestine integrity trait (VT:0010554)	colorectal tumor number (CMO:0001794)	15	2266368	22711984	Rat
1641913	Colcr2	Colorectal carcinoma resistance QTL 2	6.57	0.0197	intestine integrity trait (VT:0010554)	poorly differentiated malignant colorectal tumor number (CMO:0002076)	15	2266368	22711984	Rat
738017	Hcas7	Hepatocarcinoma susceptibility QTL 7	2.91		liver integrity trait (VT:0010547)	liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)	15	2266368	46921453	Rat
1582251	Gluco24	Glucose level QTL 24	3.2	0.0008	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	15	5530756	50530756	Rat

Markers in Region

RH141473

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	10,402,454 - 10,402,604 (+)	MAPPER	mRatBN7.2
mRatBN7.2	5	14,632,264 - 14,632,414 (-)	MAPPER	mRatBN7.2
mRatBN7.2	5	14,632,264 - 14,632,414 (+)	MAPPER	mRatBN7.2
mRatBN7.2	15	10,402,454 - 10,402,604 (-)	MAPPER	mRatBN7.2
Rnor_6.0	15	11,651,324 - 11,651,473	NCBI	Rnor6.0
Rnor_6.0	5	14,511,994 - 14,512,143	NCBI	Rnor6.0
Rnor_5.0	5	19,294,293 - 19,294,442	UniSTS	Rnor5.0
Rnor_5.0	15	15,690,037 - 15,690,186	UniSTS	Rnor5.0
RGSC_v3.4	5	14,834,856 - 14,835,005	UniSTS	RGSC3.4
RGSC_v3.4	15	11,880,859 - 11,881,008	UniSTS	RGSC3.4
Celera	15	10,412,829 - 10,412,978	UniSTS
Celera	5	14,003,484 - 14,003,633	UniSTS
Cytogenetic Map	15	p16	UniSTS
Cytogenetic Map	5	q12	UniSTS

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	43	57	41	19	41	8	10	74	35	41	11	8
Low								1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NG_081356	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003752784	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006251720	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAXUCZ010000015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000007696 ⟹ ENSRNOP00000097722

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	10,400,829 - 10,402,942 (+)	Ensembl

RefSeq Acc Id:

XM_006251720 ⟹ XP_006251782

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	15	10,401,012 - 10,403,460 (+)	NCBI
Rnor_6.0	15	11,649,874 - 11,652,109 (+)	NCBI
Rnor_5.0	15	15,688,613 - 15,690,822 (+)	NCBI

Sequence:

show sequence

TAAAAATAATATTTATGGCCGCGGGCCGAGTCTGTGAGGAAGGCCTAGGCCGTCGGCTTCGGGG
CTCGTCGAGCGTCTGCGCAGCTTCTCTCGCTTCCCGTCCGCTGTGGCCGGGAGAGAGGGGCCTT
CCGGAGCCATGGAGGACGAGGTGGTTCGCATTGCCAAGAAGATGGACAAAATGGTGCAGAAAAA
GAACGCGGCCGGTGCATTGGATTTGCTGAAAGAGCTTAAGAATATTCCCATGACCCTGGAATTA
TTACAGTCCACGAGAATTGGAATGTCTGTCAATGCTATTCGCAAGCAGAGTACAGATGAAGAAG
TCACATCTCTAGCCAAATCACTCATCAAATCCTGGAAAAAATTACTAGATGGACCATCAACTGA
TAAAGACTCTGAAGAAAAGAAAAAAGAACCTGCAATTTCATCACAGAATAGCCCTGAAGCAAGA
GAAGAAAGTAGTTCTAGCAGCCATGTAAGCAGCAGAAAGGATGAGACAAATGCTCGAGATACTT
ATGTTTCATCTTTTCCTCGGGCACCAAGCACTTCTGATTCTGTGCGGCTCAAGTGTAGGGAGAT
GCTTGCCGCAGCTCTCCGGACAGGAGATGATTATGTTGCTATTGGAGCTGATGAGGAAGAACTG
GGATCTCAGATTGAGGAAGCTATATATCAAGAAATAAGGAATACAGACATGAAATACAAAAACA
GAGTACGAAGTAGGATATCAAATCTTAAAGATGCAAAGAATCCAAATTTAAGGAAAAATGTGCT
GTGTGGGAATATTCCTCCTGACCTGTTTGCTAGAATGACAGCAGAGGAAATGGCTAGTGATGAG
CTCAAAGAGATGAGGAAAAACCTGACCAAAGAAGCCATCAGGGAGCATCAGATGGCCAAGACTG
GTGGGACCCAGACTGACTTGTTCACTTGTGGCAAATGTAAAAAGAAGAACTGCACTTACACACA
GGTGCAAACTCGTAGTGCTGATGAACCAATGACAACTTTTGTTGTATGTAATGAATGTGGAAAT
CGGTGGAAGTTCTGTTGAGTTTGGAAGAATTGGCAAGGAAGCCATGCTGTGAAGAAAATATTAG
TATCTGAGTAGAGTTCCTGGAGGCAGCATGACTGTACTTGCACTTGGAAACCTACTGACCAAGG
ATTAAGCCTGAGAACTATGTAAATTACTAAGCTGTGCTCTTTGCATATGGAGGATGCGAAAAAA
ATCCTTTAGACTGAATCTTTTGTGCTACATTTTTTCTTACATGATGATGTCAAGCCAACTGAAA
TGTAGGCTGTAGCAAGTAGTTTTACAAAACATACTTCACAATTAAGTTTTACTTTTGTTTAAAT
GTGTCCCACTTGTTTTGCTAGTACTAAGCAGTGGCTTTCACATCGTTTTCTTGACACAGACGTC
CTAATGCACAGAGCAAAGGCCACTATTTAAAGTTTACAACTTAAGTGCCTCTGCCTGTGTTCAG
ACTTCTGTGTAAAGACCACTGCACAAGCTTTGCGCTCTGCTCTGCTCTGCTCTGCTCTGCTCTG
CTCTGCTCT

hide sequence

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q4KLL0-F1-model_v2	AlphaFold	Q4KLL0	1-301	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1591965	AgrOrtholog
BioCyc Gene	G2FUF-14400	BioCyc
Ensembl Genes	ENSRNOG00000005869	Ensembl
	ENSRNOG00000022323	Ensembl
NCBI Gene	498453	ENTREZGENE
PhenoGen	Tcea1l1	PhenoGen
RatGTEx	ENSRNOG00000005869	RatGTEx
	ENSRNOG00000022323	RatGTEx

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2022-06-02	Tcea1l1	transcription elongation factor A1-like 1	AABR07017110.1		Data merged from RGD:15003306	737654	PROVISIONAL
2021-11-15	Tcea1l1	transcription elongation factor A1-like 1	LOC498453	similar to transcription elongation factor A 1 isoform 2	Name and Symbol changed	629549	APPROVED
2019-11-08	AABR07017110.1				Symbol and Name status set to provisional	45752	PROVISIONAL
2006-11-20	LOC498453	similar to transcription elongation factor A 1 isoform 2			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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