C-It-Loci: A knowledge database for tissue-enriched loci.

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Transcript Info
Description: regulatory factor X, 4 (influences HLA class II expression)
Transcript Accession Transcript Name Contained in Gene Tax ID Strand Position Biotype
ENSMUST00000060397 Rfx4-003 ENSMUSG00000020037 10090 + 10:84756062-84906144 protein_coding

Expression Patterns

Heat Map
Numeric Values
Transcript'; BrainKidneyMuscleTestisENSMUST00000060397
Transcript ID Brain Kidney Muscle Testis
ENSMUST00000060397 5.677±3.42 0.058±0.02 0.001±0.00 3.339±0.00

Conserved Regions

Region IDSub-RegionRegion TypePosition
CIL_00028K CIL_00028K_0002 CGP 10:84622437-84906538
CIL_0007NZ CIL_0007NZ_0002 UCNEbase 10:84657795-84823112
CIL_0001MF CIL_0001MF_0002 CGP 10:84756062-85016446

Gene Ontology

GO IDEvidence TypeGO Description
GO:0003677 IEA DNA binding
GO:0003682 IDA chromatin binding
GO:0005515 IPI protein binding
GO:0005634 IDA nucleus
GO:0006351 IEA transcription, DNA-templated
GO:0006357 IDA regulation of transcription from RNA polymerase II promoter
GO:0021516 IMP dorsal spinal cord development
GO:0021537 IMP telencephalon development
GO:0021696 IMP cerebellar cortex morphogenesis
GO:0021914 IMP negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning
GO:0030900 IMP forebrain development
GO:0030901 IMP midbrain development
GO:0042384 IMP cilium assembly
GO:0045944 IDA positive regulation of transcription from RNA polymerase II promoter
GO:0070613 IMP regulation of protein processing

Homologs

ENSEMBL Accession Gene Name Biotype Species E-Value Bit Score
ENSDART00000031752 rfx4-001 protein_coding Danio_rerio 0 1195
ENST00000229387 RFX4-001 protein_coding Homo_sapiens 0 3048
ENST00000357881 RFX4-003 protein_coding Homo_sapiens 0 2987
ENST00000392842 RFX4-002 protein_coding Homo_sapiens 0 3999
ENST00000536688 RFX4-006 retained_intron Homo_sapiens 0 2067
ENST00000536722 RFX4-005 nonsense_mediated_decay Homo_sapiens 0 885
ENST00000539967 RFX4-004 protein_coding Homo_sapiens 0 586
ENST00000546882 RFX4-008 nonsense_mediated_decay Homo_sapiens 0 261
ENST00000549040 RFX4-009 protein_coding Homo_sapiens 0 538
ENST00000551640 RFX4-010 protein_coding Homo_sapiens 0 1031
ENST00000552773 RFX4-007 retained_intron Homo_sapiens 0 357
ENST00000552866 RFX4-011 protein_coding Homo_sapiens 0 401
ENST00000552917 RFX4-012 nonsense_mediated_decay Homo_sapiens 0 691

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