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

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Gene Info

Description: collagen, type II, alpha 1
Gene AccessionGene NameTax IDStrandPositionGene Biotype
ENSG00000139219 COL2A1 9606 - 12:47972965-48004486 protein_coding
  Transcript Accession Transcript Name Position Transcript Biotype
  ENST00000337299 COL2A1-008 47973407-48004321 protein_coding
  ENST00000380518 COL2A1-001 47972965-48004486 protein_coding
  ENST00000465743 COL2A1-005 48002622-48004362 processed_transcript
  ENST00000466884 COL2A1-004 47998169-47998859 processed_transcript
  ENST00000474996 COL2A1-002 47997615-48004449 processed_transcript
  ENST00000483376 COL2A1-006 47981343-47983855 retained_intron
  ENST00000490609 COL2A1-003 47999697-48004486 retained_intron
  ENST00000493991 COL2A1-007 47973201-47988471 processed_transcript
  ENST00000546974 COL2A1-009 47975353-47977445 retained_intron

Homo sapiens EnsemblGRCh38

Genome
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Genes
Gene structures from Ensembl
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Transcripts
Structures from Ensembl
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Expression Patterns

Heat Map
Numeric Values
Transcript'; AdrenalBrainBreastColonHeartLiverLungMuscleOvaryPlacentaTestisENST00000337299ENST00000380518ENST00000474996ENST00000490609ENST00000493991ENST00000546974
Transcript ID Adrenal Brain Breast Colon Heart Liver Lung Muscle Ovary Placenta Testis
ENST00000337299 N/A 0.029±0.00 N/A N/A N/A N/A N/A N/A 0.015±0.00 N/A 0.245±0.00
ENST00000380518 N/A N/A 0.102±0.00 N/A N/A N/A 0.088±0.00 N/A 0.550±0.22 0.279±0.06 0.385±0.27
ENST00000474996 N/A 0.072±0.00 N/A N/A N/A N/A N/A N/A N/A N/A N/A
ENST00000490609 N/A N/A N/A N/A N/A 0.404±0.00 N/A N/A 0.225±0.00 N/A N/A
ENST00000493991 0.015±0.00 0.075±0.01 0.029±0.00 0.037±0.00 0.007±0.00 0.036±0.00 N/A 0.032±0.00 N/A 0.105±0.04 N/A
ENST00000546974 N/A N/A N/A 0.099±0.00 N/A N/A N/A N/A N/A 0.537±0.22 N/A

Conserved Regions

Region IDSub-RegionRegion TypePosition
CIL_0005YL CIL_0005YL_0001 CGP 12:47963569-48004486
CIL_00079B CIL_00079B_0001 CGP 12:47972965-48106308

Gene Ontology
GO IDEvidence TypeGO Description
GO:0001501 IMP skeletal system development
GO:0001502 IEA cartilage condensation
GO:0001503 IEA ossification
GO:0001894 IEA tissue homeostasis
GO:0001958 IEA endochondral ossification
GO:0002062 IEA chondrocyte differentiation
GO:0003007 IEA heart morphogenesis
GO:0005201 IEA extracellular matrix structural constituent
GO:0005515 IEA protein binding
GO:0005576 TAS extracellular region
GO:0005578 IEA proteinaceous extracellular matrix
GO:0005581 IEA collagen trimer
GO:0005585 IDA collagen type II trimer
GO:0005604 IEA basement membrane
GO:0005615 IEA extracellular space
GO:0005737 IEA cytoplasm
GO:0005788 TAS endoplasmic reticulum lumen
GO:0006029 IEA proteoglycan metabolic process
GO:0007411 TAS axon guidance
GO:0007417 IEA central nervous system development
GO:0007601 IMP visual perception
GO:0007605 IMP sensory perception of sound
GO:0010468 IEA regulation of gene expression
GO:0022617 TAS extracellular matrix disassembly
GO:0030020 IC extracellular matrix structural constituent conferring tensile strength
GO:0030198 TAS extracellular matrix organization
GO:0030199 IMP collagen fibril organization
GO:0030574 TAS collagen catabolic process
GO:0030903 IEA notochord development
GO:0031012 IDA extracellular matrix
GO:0035108 IEA limb morphogenesis
GO:0042472 IEA inner ear morphogenesis
GO:0042802 NAS identical protein binding
GO:0046872 IEA metal ion binding
GO:0048407 IDA platelet-derived growth factor binding
GO:0048705 IEA skeletal system morphogenesis
GO:0048839 IEA inner ear development
GO:0051216 TAS cartilage development
GO:0060021 IEA palate development
GO:0060174 IEA limb bud formation
GO:0060272 IMP embryonic skeletal joint morphogenesis
GO:0060348 IEA bone development
GO:0060351 IEA cartilage development involved in endochondral bone morphogenesis
GO:0071599 IEA otic vesicle development
GO:0071773 IEA cellular response to BMP stimulus
GO:2001240 IEA negative regulation of extrinsic apoptotic signaling pathway in absence of ligand

Homologs

ENSEMBL Accession Gene Name Description Biotype Species
ENSDARG00000011407 col2a1b collagen type II, alpha-1b protein_coding Danio_rerio
ENSDARG00000069093 col2a1a collagen type II, alpha-1a protein_coding Danio_rerio
ENSMUSG00000022483 Col2a1 collagen, type II, alpha 1 protein_coding Mus_musculus

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