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

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Transcript Info
Description: collagen, type II, alpha 1
Transcript Accession Transcript Name Contained in Gene Tax ID Strand Position Biotype
ENST00000380518 COL2A1-001 ENSG00000139219 9606 - 12:47972965-48004486 protein_coding

Homo sapiens EnsemblGRCh38

Genome
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Structures from Ensembl
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Transcripts
Structures from Ensembl
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Expression Patterns

Heat Map
Numeric Values
Transcript'; BreastLungOvaryPlacentaTestisENST00000380518
Transcript ID Breast Lung Ovary Placenta Testis
ENST00000380518 0.102±0.00 0.088±0.00 0.550±0.22 0.279±0.06 0.385±0.27

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 Biotype Species E-Value Bit Score
ENSMUST00000023123 Col2a1-001 protein_coding Mus_musculus 0 6263
ENSMUST00000088355 Col2a1-002 protein_coding Mus_musculus 0 5696
ENSDART00000015092 col1a1b-001 protein_coding Danio_rerio 0 955
ENSMUST00000139246 Col2a1-006 retained_intron Mus_musculus 0 730
ENSMUST00000133488 Col2a1-005 processed_transcript Mus_musculus 0 658
ENSMUST00000131910 Col2a1-008 retained_intron Mus_musculus 0 525
ENSDART00000042990 col1a2-201 protein_coding Danio_rerio 0 254
ENSDART00000144544 col1a2-001 protein_coding Danio_rerio 0 254
ENSMUST00000031668 Col1a2-001 protein_coding Mus_musculus 3e-39 169

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