Pathway Human Homo sapiens

Collagen formation

R-HSA-1474290 in Reactome release 97: under Extracellular matrix organization, with 90 genes placed in it by the mapping files and 2 child pathways in the hierarchy.

The same number in the other species

Reactome writes the mouse and rat events it infers from a human pathway under the human number with the species token. A door opens only where that species' own list in this release holds the id: R-MMU-1474290 (mouse), R-RNO-1474290 (rat). Whether the event was inferred from this one is what the record says.

The record
The genes
Parents and children

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This page reads the pathway's record from its source while you read the rest; with scripts off the card stays at its loading line. Reload with scripts on to see it, or open the source's own page from the link in the card.

01The record

Reactome's own record of this pathway

What this tells you

The pathway list, the hierarchy and the genes on this page are read from the files Reactome publishes for Reactome release 97, built into this site on 2026-09-09: the pathway list, the hierarchy relationship file and the two gene mapping files. The record card is the one live read, Reactome's own record of this pathway.

Reactome's download page describes the mapping files: Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway, all levels of the pathway hierarchy or database identifier to all reactions. [R13] The gene list here is the all-levels mapping of NCBI Gene ids, filled from the all-levels mapping of Ensembl ids where the NCBI file has no row for a gene; each row names which file it came from by the shape of its source id. Each row carries the evidence codes the file writes for it, as written and unranked, and both where the file writes both; no page of Reactome's documentation the survey read defines the codes, so this page does not expand them. A gene id the identity files do not name is kept as the source's own id with no door rather than turned into a symbol.

On citing what a search finds, Reactome says: It should be remembered that while we strive to contain the most current and accurate data, Reactome should not be used in citations where other primary sources of information are available. [R12] The record card prints the literature Reactome attaches to a curated pathway for that reason. The data are public domain: All data in the Reactome database and files derived from that data are licensed under the Creative Commons Public Domain Dedication (CC0). User may copy, modify, and distribute these data, even for commercial purposes, without asking for permission. Attribution is encouraged but not required. [R10] The pathway illustrations are licensed apart, under CC BY 4.0, and none is shown here.

A gene on this list is one Reactome places in this pathway in this release, and that is all the row says: it does not say the gene is expressed in a tissue or associated with a disease, which are the other two explorers' questions, read from other sources. Reactome's papers of record are [R01] [R02].

[R01] Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, et al. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Research 54:D673-D681. PMID 41251150, doi 10.1093/nar/gkaf1223.
[R02] Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, et al. (2024). The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research 52:D672-D678. PMID 37941124, doi 10.1093/nar/gkad1025.
[R10] Reactome, reactome.org. License Agreement. https://reactome.org/license, read 2026-09-09.
[R12] Reactome, reactome.org. Citing us. https://reactome.org/cite, read 2026-09-09.
[R13] Reactome, reactome.org. Download. https://reactome.org/download-data, read 2026-09-09.

Stable id: R-HSA-1474290.5
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: no
Released: 2012-06-12
Last updated: 2017-12-18
Events inside: 2, counted from the record

Collagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in mammals making up about 25% to 35% of whole-body protein content. A defining feature of collagens is the formation of trimeric left-handed polyproline II-type helical collagenous regions. The packing within these regions is made possible by the presence of the smallest amino acid, glycine, at every third residue, resulting in a repeating motif Gly-X-Y where X is often proline (Pro) and Y often 4-hydroxyproline (4Hyp). Gly-Pro-Hyp is the most common triplet in collagen (Ramshaw et al. 1998). Collagen peptide chains also have non-collagenous domains, with collagen subclasses having common chain structures. Collagen fibrils are mostly found in fibrous tissues such as tendon, ligament and skin. Other forms of collagen are abundant in cornea, cartilage, bone, blood vessels, the gut, and intervertebral disc. In muscle tissue, collagen is a major component of the endomysium, constituting up to 6% of muscle mass. Gelatin, used in food and industry, is collagen that has been irreversibly hydrolyzed. On the basis of their fibre architecture in tissues, the genetically distinct collagens have been divided into subgroups. Group 1 collagens have uninterrupted triple-helical domains of about 300 nm, forming large extracellular fibrils. They are referred to as the fibril-forming collagens, consisting of collagens types I, II, III, V, XI, XXIV and XXVII. Group 2 collagens are types IV and VII, which have extended triple helices (>350 nm) with imperfections in the Gly-X-Y repeat sequences. Group 3 are the short-chain collagens. These have two subgroups. Group 3A have continuous triple-helical domains (type VI, VIII and X). Group 3B have interrupted triple-helical domains, referred to as the fibril-associated collagens with interrupted triple helices (FACIT collagens, Shaw & Olsen 1991). FACITs include collagen IX, XII, XIV, XVI, XIX, XX, XXI, XXII and XXVI plus the transmembrane collagens (XIII, XVII, XXIII and XXV) and the multiple triple helix domains and interruptions (Multiplexin) collagens XV and XVIII (Myllyharju & Kivirikko 2004). The non-collagenous domains of collagens have regulatory functions; several are biologically active when cleaved from the main peptide chain. Fibrillar collagen peptides all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N- and C-propeptides, which are cleaved prior to formation of the collagen fibril. The intact form is referred to as a collagen propeptide, not procollagen, which is used to refer to the trimeric triple-helical precursor of collagen before the propeptides are removed. The C-propeptide, also called the NC1 domain, directs chain association during assembly of the procollagen molecule from its three constituent alpha chains (Hulmes 2002).

Fibril forming collagens are the most familiar and best studied subgroup. Collagen fibres are aggregates or bundles of collagen fibrils, which are themselves polymers of tropocollagen complexes, each consisting of three polypeptide chains known as alpha chains. Tropocollagens are considered the subunit of larger collagen structures. They are approximately 300 nm long and 1.5 nm in diameter, with a left-handed triple-helical structure, which becomes twisted into a right-handed coiled-coil 'super helix' in the collagen fibril. Tropocollagens in the extracellular space polymerize spontaneously with regularly staggered ends (Hulmes 2002). In fibrillar collagens the molecules are staggered by about 67 nm, a unit known as D that changes depending upon the hydration state. Each D-period contains slightly more than four collagen molecules so that every D-period repeat of the microfibril has a region containing five molecules in cross-section, called the 'overlap', and a region containing only four molecules, called the 'gap'. The triple-helices are arranged in a hexagonal or quasi-hexagonal array in cross-section, in both the gap and overlap regions (Orgel et al. 2006). Collagen molecules cross-link covalently to each other via lysine and hydroxylysine side chains. These cross-links are unusual, occuring only in collagen and elastin, a related protein.

The macromolecular structures of collagen are diverse. Several group 3 collagens associate with larger collagen fibers, serving as molecular bridges which stabilize the organization of the extracellular matrix. Type IV collagen is arranged in an interlacing network within the dermal-epidermal junction and vascular basement membranes. Type VI collagen forms distinct microfibrils called beaded filaments. Type VII collagen forms anchoring fibrils. Type VIII and X collagens form hexagonal networks. Type XVII collagen is a component of hemidesmosomes where it is complexed wtih alpha6Beta4 integrin, plectin, and laminin-332 (de Pereda et al. 2009). Type XXIX collagen has been recently reported to be a putative epidermal collagen with highest expression in suprabasal layers (Soderhall et al. 2007). Collagen fibrils/aggregates arranged in varying combinations and concentrations in different tissues provide specific tissue properties. In bone, collagen triple helices lie in a parallel, staggered array with 40 nm gaps between the ends of the tropocollagen subunits, which probably serve as nucleation sites for the deposition of crystals of the mineral component, hydroxyapatite (Ca10(PO4)6(OH)2) with some phosphate. Collagen structure affects cell-cell and cell-matrix communication, tissue construction in growth and repair, and is changed in development and disease (Sweeney et al. 2006, Twardowski et al. 2007). A single collagen fibril can be heterogeneous along its axis, with significantly different mechanical properties in the gap and overlap regions, correlating with the different molecular organizations in these regions (Minary-Jolandan & Yu 2009).

Literature Reactome attaches

Collagens: molecular biology, diseases, and potentials for therapyAnnu Rev Biochem, 1995, vol. 64, p. 403-34PubMed 7574488
CollagensCell Tissue Res, 2010, vol. 339, p. 247-57PubMed 19693541

Reactome's record lists 11 orthologous events, R-RNO-1474290 (Rattus norvegicus), R-MMU-1474290 (Mus musculus) among the species this site serves, and 9 in species this site opens no page for.

Reactome ContentService, this pathway's record · Reactome v97 · read 2026-09-30 ET · Reactome pathway browser"Collagen formation". Reactome, release 97, https://reactome.org/PathwayBrowser/#/R-HSA-1474290 with StableID: R-HSA-1474290.5 (accessed 2026-09-30 ET). Reactome version 97 (CC0).

Reading this pathway's record from Reactome (the pathway record).Still reading. A first read of a pathway can take a while; this page waits up to 35 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.

02The genes

Genes Reactome places in this human pathway

The mapping files place 90 genes in this human pathway; showing 1 to 90, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 1 of 1
Gene	Authority id	Mapping file id	Evidence codes
GeneADAMTS14	AuthorityHGNC:14899	Mapping file id140766 NCBI file	EvidenceTAS
GeneADAMTS2	AuthorityHGNC:218	Mapping file id9509 NCBI file	EvidenceTAS
GeneADAMTS3	AuthorityHGNC:219	Mapping file id9508 NCBI file	EvidenceTAS
GeneBMP1	AuthorityHGNC:1067	Mapping file id649 NCBI file	EvidenceTAS
GeneCD151	AuthorityHGNC:1630	Mapping file id977 NCBI file	EvidenceTAS
GeneCOL10A1	AuthorityHGNC:2185	Mapping file id1300 NCBI file	EvidenceTAS
GeneCOL11A1	AuthorityHGNC:2186	Mapping file id1301 NCBI file	EvidenceTAS
GeneCOL11A2	AuthorityHGNC:2187	Mapping file id1302 NCBI file	EvidenceTAS
GeneCOL12A1	AuthorityHGNC:2188	Mapping file id1303 NCBI file	EvidenceTAS
GeneCOL13A1	AuthorityHGNC:2190	Mapping file id1305 NCBI file	EvidenceTAS
GeneCOL14A1	AuthorityHGNC:2191	Mapping file id7373 NCBI file	EvidenceTAS
GeneCOL15A1	AuthorityHGNC:2192	Mapping file id1306 NCBI file	EvidenceTAS
GeneCOL16A1	AuthorityHGNC:2193	Mapping file id1307 NCBI file	EvidenceTAS
GeneCOL17A1	AuthorityHGNC:2194	Mapping file id1308 NCBI file	EvidenceTAS
GeneCOL18A1	AuthorityHGNC:2195	Mapping file id80781 NCBI file	EvidenceTAS
GeneCOL19A1	AuthorityHGNC:2196	Mapping file id1310 NCBI file	EvidenceTAS
GeneCOL1A1	AuthorityHGNC:2197	Mapping file id1277 NCBI file	EvidenceTAS
GeneCOL1A2	AuthorityHGNC:2198	Mapping file id1278 NCBI file	EvidenceTAS
GeneCOL20A1	AuthorityHGNC:14670	Mapping file id57642 NCBI file	EvidenceTAS
GeneCOL21A1	AuthorityHGNC:17025	Mapping file id81578 NCBI file	EvidenceTAS
GeneCOL22A1	AuthorityHGNC:22989	Mapping file id169044 NCBI file	EvidenceTAS
GeneCOL23A1	AuthorityHGNC:22990	Mapping file id91522 NCBI file	EvidenceTAS
GeneCOL24A1	AuthorityHGNC:20821	Mapping file id255631 NCBI file	EvidenceTAS
GeneCOL25A1	AuthorityHGNC:18603	Mapping file id84570 NCBI file	EvidenceTAS
GeneCOL26A1	AuthorityHGNC:18038	Mapping file id136227 NCBI file	EvidenceTAS
GeneCOL27A1	AuthorityHGNC:22986	Mapping file id85301 NCBI file	EvidenceTAS
GeneCOL28A1	AuthorityHGNC:22442	Mapping file id340267 NCBI file	EvidenceTAS
GeneCOL2A1	AuthorityHGNC:2200	Mapping file id1280 NCBI file	EvidenceTAS
GeneCOL3A1	AuthorityHGNC:2201	Mapping file id1281 NCBI file	EvidenceTAS
GeneCOL4A1	AuthorityHGNC:2202	Mapping file id1282 NCBI file	EvidenceTAS
GeneCOL4A2	AuthorityHGNC:2203	Mapping file id1284 NCBI file	EvidenceTAS
GeneCOL4A3	AuthorityHGNC:2204	Mapping file id1285 NCBI file	EvidenceTAS
GeneCOL4A4	AuthorityHGNC:2206	Mapping file id1286 NCBI file	EvidenceTAS
GeneCOL4A5	AuthorityHGNC:2207	Mapping file id1287 NCBI file	EvidenceTAS
GeneCOL4A6	AuthorityHGNC:2208	Mapping file id1288 NCBI file	EvidenceTAS
GeneCOL5A1	AuthorityHGNC:2209	Mapping file id1289 NCBI file	EvidenceTAS
GeneCOL5A2	AuthorityHGNC:2210	Mapping file id1290 NCBI file	EvidenceTAS
GeneCOL5A3	AuthorityHGNC:14864	Mapping file id50509 NCBI file	EvidenceTAS
GeneCOL6A1	AuthorityHGNC:2211	Mapping file id1291 NCBI file	EvidenceTAS
GeneCOL6A2	AuthorityHGNC:2212	Mapping file id1292 NCBI file	EvidenceTAS
GeneCOL6A3	AuthorityHGNC:2213	Mapping file id1293 NCBI file	EvidenceTAS
GeneCOL6A5	AuthorityHGNC:26674	Mapping file id256076 NCBI file	EvidenceTAS
GeneCOL6A6	AuthorityHGNC:27023	Mapping file id131873 NCBI file	EvidenceTAS
GeneCOL7A1	AuthorityHGNC:2214	Mapping file id1294 NCBI file	EvidenceTAS
GeneCOL8A1	AuthorityHGNC:2215	Mapping file id1295 NCBI file	EvidenceTAS
GeneCOL8A2	AuthorityHGNC:2216	Mapping file id1296 NCBI file	EvidenceTAS
GeneCOL9A1	AuthorityHGNC:2217	Mapping file id1297 NCBI file	EvidenceTAS
GeneCOL9A2	AuthorityHGNC:2218	Mapping file id1298 NCBI file	EvidenceTAS
GeneCOL9A3	AuthorityHGNC:2219	Mapping file id1299 NCBI file	EvidenceTAS
GeneCOLGALT1	AuthorityHGNC:26182	Mapping file id79709 NCBI file	EvidenceTAS
GeneCOLGALT2	AuthorityHGNC:16790	Mapping file id23127 NCBI file	EvidenceTAS
GeneCRTAP	AuthorityHGNC:2379	Mapping file id10491 NCBI file	EvidenceTAS
GeneCTSB	AuthorityHGNC:2527	Mapping file id1508 NCBI file	EvidenceTAS
GeneCTSL	AuthorityHGNC:2537	Mapping file id1514 NCBI file	EvidenceTAS
GeneCTSS	AuthorityHGNC:2545	Mapping file id1520 NCBI file	EvidenceTAS
GeneCTSV	AuthorityHGNC:2538	Mapping file id1515 NCBI file	EvidenceTAS
GeneDST	AuthorityHGNC:1090	Mapping file id667 NCBI file	EvidenceTAS
GeneITGA6	AuthorityHGNC:6142	Mapping file id3655 NCBI file	EvidenceTAS
GeneITGB4	AuthorityHGNC:6158	Mapping file id3691 NCBI file	EvidenceTAS
GeneLAMA3	AuthorityHGNC:6483	Mapping file id3909 NCBI file	EvidenceTAS
GeneLAMB3	AuthorityHGNC:6490	Mapping file id3914 NCBI file	EvidenceTAS
GeneLAMC2	AuthorityHGNC:6493	Mapping file id3918 NCBI file	EvidenceTAS
GeneLOX	AuthorityHGNC:6664	Mapping file id4015 NCBI file	EvidenceTAS
GeneLOXL1	AuthorityHGNC:6665	Mapping file id4016 NCBI file	EvidenceTAS
GeneLOXL2	AuthorityHGNC:6666	Mapping file id4017 NCBI file	EvidenceTAS
GeneLOXL3	AuthorityHGNC:13869	Mapping file id84695 NCBI file	EvidenceTAS
GeneLOXL4	AuthorityHGNC:17171	Mapping file id84171 NCBI file	EvidenceTAS
GeneMMP13	AuthorityHGNC:7159	Mapping file id4322 NCBI file	EvidenceTAS
GeneMMP20	AuthorityHGNC:7167	Mapping file id9313 NCBI file	EvidenceTAS
GeneMMP3	AuthorityHGNC:7173	Mapping file id4314 NCBI file	EvidenceTAS
GeneMMP7	AuthorityHGNC:7174	Mapping file id4316 NCBI file	EvidenceTAS
GeneMMP9	AuthorityHGNC:7176	Mapping file id4318 NCBI file	EvidenceTAS
GeneP3H1	AuthorityHGNC:19316	Mapping file id64175 NCBI file	EvidenceTAS
GeneP3H2	AuthorityHGNC:19317	Mapping file id55214 NCBI file	EvidenceTAS
GeneP3H3	AuthorityHGNC:19318	Mapping file id10536 NCBI file	EvidenceTAS
GeneP4HA1	AuthorityHGNC:8546	Mapping file id5033 NCBI file	EvidenceTAS
GeneP4HA2	AuthorityHGNC:8547	Mapping file id8974 NCBI file	EvidenceTAS
GeneP4HA3	AuthorityHGNC:30135	Mapping file id283208 NCBI file	EvidenceTAS
GeneP4HB	AuthorityHGNC:8548	Mapping file id5034 NCBI file	EvidenceTAS
GenePCOLCE	AuthorityHGNC:8738	Mapping file id5118 NCBI file	EvidenceTAS
GenePCOLCE2	AuthorityHGNC:8739	Mapping file id26577 NCBI file	EvidenceTAS
GenePLEC	AuthorityHGNC:9069	Mapping file id5339 NCBI file	EvidenceTAS
GenePLOD1	AuthorityHGNC:9081	Mapping file id5351 NCBI file	EvidenceTAS
GenePLOD2	AuthorityHGNC:9082	Mapping file id5352 NCBI file	EvidenceTAS
GenePLOD3	AuthorityHGNC:9083	Mapping file id8985 NCBI file	EvidenceTAS
GenePPIB	AuthorityHGNC:9255	Mapping file id5479 NCBI file	EvidenceTAS
GenePXDN	AuthorityHGNC:14966	Mapping file id7837 NCBI file	EvidenceTAS
GeneSERPINH1	AuthorityHGNC:1546	Mapping file id871 NCBI file	EvidenceTAS
GeneTLL1	AuthorityHGNC:11843	Mapping file id7092 NCBI file	EvidenceTAS
GeneTLL2	AuthorityHGNC:11844	Mapping file id7093 NCBI file	EvidenceTAS

Evidence codes on this page: TAS, as the mapping file writes them; a row carrying two was written twice by the file, once under each. The mapping file id says which file placed the gene: an NCBI Gene id from NCBI2Reactome_All_Levels.txt, an Ensembl gene id from Ensembl2Reactome_All_Levels.txt. The two files can disagree about a code, so a row's codes are the one file's view. Measured by this site's build over this release on 2026-09-09: of the 138,908 human pathway-gene pairs both files place, 207 (0.149 per cent, over 47 genes) carry TAS in the Ensembl file where the NCBI rows carry IEA alone.

Reactome mapping files, the human rows for this pathway · Reactome release 97 · read 2026-09-09 · Reactome downloads"NCBI2Reactome_All_Levels.txt" and "Ensembl2Reactome_All_Levels.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.

03The hierarchy

Parents and children in this release's hierarchy

Parents

Extracellular matrix organizationR-HSA-1474244321 genes

Children

Reactome's hierarchy is a graph rather than a tree: a pathway can sit under more than one parent, and the gene counts are each pathway's own placements at every level under it, so a parent's count is not the sum of its children's.

Reactome, the human pathway list and hierarchy relationship file · Reactome release 97 · read 2026-09-09 · Reactome downloads"ReactomePathways.txt" and "ReactomePathwaysRelation.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.