Tumor Endothelial Marker Report: TEM31_1 (alpha1(IV) collagen)

TEM domain structure

	TEM domain structure

TEM Sequence Analysis

name from to source/E description

SignalP 1 28 SignalP

21x collagen triple helix repeats 43 1425 PFAM, E = 7.8e-196 The region is comprised of 21 copies of the PFAM collagen domain, the latter containing 20 copies of the G-X-Y repeat.

28 172 7S domain The 7S domain of the alpha 1 (IV) chain starts with a non-triple-helical region containing four cysteine and two lysine residues and mediates the formation of the tetramers collagen suprastructure. The following 120-residue-long triple helical segment is involved in triple helix formation.

172 1425 19x
collagen The segment is involved in triple helix formation.

C4 1445 1554 PFAM, E = 4.1e-73 This domain is found to be duplicated in the C-terminus of type 4 collagens. Three alpha-chains self-assemble to form a monomer of an extracellular network. The NCI domain is important for helical formation and also for assembly of collagen monomers into dimers.

C4 1555 1668 PFAM, E = 3e-76 This domain is found to be duplicated in the C-terminus of type 4 collagens. Three alpha-chains self-assemble to form a monomer of an extracellular network. The NCI domain is important for helical formation and also for assembly of collagen monomers into dimers.

	TEM Sequence Analysis

name	from	to	source/E	description
SignalP	1	28	SignalP
21x collagen triple helix repeats	43	1425	PFAM, E = 7.8e-196	The region is comprised of 21 copies of the PFAM collagen domain, the latter containing 20 copies of the G-X-Y repeat.
	28	172	7S domain	The 7S domain of the alpha 1 (IV) chain starts with a non-triple-helical region containing four cysteine and two lysine residues and mediates the formation of the tetramers collagen suprastructure. The following 120-residue-long triple helical segment is involved in triple helix formation.
	172	1425	19x collagen	The segment is involved in triple helix formation.
C4	1445	1554	PFAM, E = 4.1e-73	This domain is found to be duplicated in the C-terminus of type 4 collagens. Three alpha-chains self-assemble to form a monomer of an extracellular network. The NCI domain is important for helical formation and also for assembly of collagen monomers into dimers.
C4	1555	1668	PFAM, E = 3e-76	This domain is found to be duplicated in the C-terminus of type 4 collagens. Three alpha-chains self-assemble to form a monomer of an extracellular network. The NCI domain is important for helical formation and also for assembly of collagen monomers into dimers.

Remarks

	Remarks

RELIABILITY:
CONTRA: The inverse localization of the tag and the unreliable Cid->Tag frequency make the tag to gen mapping unreliable.
PRO: Another SAGE tag potential derived from alpha1 (IV) collagen has been found in the experiment (PEM59) and shows a N-ECs/T-ECs ratio not too divergent from the one observed for TEM31_1.
CLASSIFICATION: Non-fibrillar collagen.
DOMAIN ARCHITECTURE: Collagen alpha 1(IV) shows three structural domains: the 7S propeptide-, the triple helical- and the noncollagenous NC1 segment).
FUNCTION: Type IV collagens localize in basement membranes and there are six types: alpha1 through alpha6. The major type IV collagens in most basement membranes are alpha1 and alpha2, whereas alpha3, alpha4, and alpha5 predominate in the GBM.
Basement membrane type IV collagen provides tensile strength and scaffolding for the binding and alignment of other basement membrane molecules, like laminin, entactin, proteoglycan and fibronectin.
Type IV collagen has been implicated in the regulation of angiogenesis and is proposed to act in vascular elongation, proliferation and stabilization.

Sequence Information

TEM TEM31_1

Reliability of Gen2Tag mapping

Cid->tag (Hs.119129) frequency:
       : CATG-GACCGCAGGA=110/154 (Est oriented)
PEM59  : CATG-GTGCTACTTC=23/154 (Est oriented)
tem31_1: CATG-AGAAACCACGG=4/154 (Est oriented)

tag occurrence in N-ECs/T-ECs/HUVEC/HMVEC:
PEM59  : CATG-GTGCTACTTCT=5/25/2/18
tem31_1: CATG-AGAAACCACGG=0/8/2/7

REMARKS: Tag/ Hs.119129 COL4A1:
The Tag is not derived reliably from Hs.119129, see mRNA description.

Analysis
Output Created by a Suite of Single Sequence Analysis Techniques

Protein Description

SEQ.SOURCE: sp|P02462|CA14_collagen alpha 1(IV)

Protein Sequence

MGPRLSVWLLLLPAALLLHEEHSRAAAKGGCAGSGCGKCDCHGVKGQKGERGLPGLQGVIGFPGMQGPEG PQGPPGQKGDTGEPGLPGTKGTRGPPGASGYPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGL PGFAGNPGPPGLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPGFTGPPGPPGP PGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQAQVQEKGDFATKGEKGQKGEPGFQGMPGVGEKGEP GKPGPRGKPGKDGDKGEKGSPGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPG TPGPRGEPGPKGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPGTSLPGPSGRDGLPGPPGSPG PPGQPGYTNGIVECQPGPPGDQGPPGIPGQPGFIGEIGEKGQKGESCLICDIDGYRGPPGPQGPPGEIGF PGQPGAKGDRGLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLKGDKGDPGFPGQPGMPGRAGS PGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDTGPPGPPGYGPAGPIGDKGQAGFPGGPGSPG LPGPKGEPGKIVPLPGPPGAEGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPGIGFPGPPGPKGV DGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEPGVGLPGLKGLPGLPGIPGTPGEKGSIGVPGVPGEHG AIGPPGLQGIRGEPGPPGLPGSVGSPGVPGIGPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLDMPG PKGDKGAQGLPGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPGLPGEKGDHGF PGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQKGDQGEKGQIGPIGEKGSRGDPGTPGVPGKD GQAGQPGQPGPKGDPGISGTPGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGDKGAKGEKG QAGPPGIGIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKGSPGSVGYPGSPGLPGEKGDK GLPGLDGIPGVKGEAGLPGTPGPTGPAGQKGEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGE VGFPGLAGSPGIPGSKGEQGFMGPPGPQGQPGLPGSPGHATEGPKGDRGPQGQPGLPGLPGPMGPPGLPG IDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGITGSKGDMGPPGVPGFQGPKGLPGLQGIKGD QGDQGVPGAKGLPGPPGPPGPYDIIKGEPGLPGPEGPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGF DGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTPSVDHGFLVTRHSQTIDDPQCPSGTKILYHG YSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGEN IRPFISRCAVCEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRS APFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT

SAGE-Tag CATG-AGAAACCACGG

EST/cluster Description

UNIGEN CLUSTER: Hs.119129 : collagen, type IV, alpha 1

SEQ.SOURCE: gi|180422|gb|M10941.1|HUMCG4A12 Human procollagen type IV alpha-1 chain 3 UTR

Remark: The Tag is in the 3 UTR of COL4A1 but is oriented inversly, and thus is probably not the derived from COL4A1

ANALYSIS: BLASTN against ESTDB=4 ESTs seem to have their terminus in around the proposed PolyA-signal of the Tag

MARKINGS: TEM31_1 Tag in red
PEM59 Tag in red
first Poly-A-signal following the tem31_2 Tag in bold

EST/cluster Sequence

CCTGGGATTGATGGAGTTAAAGGTGACAAAGGAAATCCAGGCTGGCCAGGAGCACCCGGT GTCCCAGGGCCCAAGGGAGACCCTGGATTCCAGGGCATGCCTGGTATTGGTGGCTCTCCA GGAATCACAGGCTCTAAGGGTGATATGGGGCCTCCAGGAGTTCCAGGATTTCAAGGTCCA AAAGGTCTTCCTGGCCTCCAGGGAATTAAAGGTGATCAAGGCGATCAAGGCGTCCCGGGA GCTAAAGGTCTCCCGGGTCCTCCTGGCCCCCCAGGTCCTTACGACATCATCAAAGGGGAG CCCGGGCTCCCTGGTCCTGAGGGCCCCCCAGGGCTGAAAGGGCTTCAGGGACTGCCAGGC CCGAAAGGCCAGCAAGGTGTTACAGGATTGGTGGGTATACCTGGACCTCCAGGTATTCCT GGGTTTGACGGTGCCCCTGGCCAGAAAGGAGAGATGGGACCTGCCGGGCCTACTGGTCCA AGAGGATTTCCAGGTCCACCAGGCCCCGATGGGTTGCCAGGATCCATGGGGCCTCCAGGC ACCCCATCTGTTGATCACGGCTTCCTTGTGACCAGGCATAGTCAAACAATAGATGACCCA CAGTGTCCTTCTGGGACCAAAATTCTTTACCACGGGTACTCTTTGCTCTACGTGCAAGGC AATGAACGGGCCCATGGCCAGGACTTGGGCACGGCCGGCAGCTGCCTGCGCAAGTTCAGC ACAATGCCCTTCCTGTTCTGCAATATTAACAACGTGTGCAACTTTGCATCACGAAATGAC TACTCGTACTGGCTGTCCACCCCTGAGCCCATGCCCATGTCAATGGCACCCATCACGGGG GAAAACATAAGACCATTTATTAGTAGGTGTGCTGTGTGTGAGGCGCCTGCCATGGTGATG GCCGTGCACAGCCAGACCATTCAGATCCCACCGTGCCCCAGCGGGTGGTCCTCGCTGTGG ATCGGCTACTCTTTTGTGATGCACACCAGCGCTGGTGCAGAAGGCTCTGGCCAAGCCCTG GCGTCCCCCGGCTCCTGCCTGGAGGAGTTTAGAAGTGCGCCATTCATCGAGTGTCACGGC CGTGGGACCTGCAATTACTACGCAAACGCTTACAGCTTTTGGCTCGCCACCATAGAGAGG AGCGAGATGTTCAAGAAGCCTACGCCGTCCACCTTGAAGGCAGGGGAGCTGCGCACGCAC GTCAGCCGCTGCCAAGTCTGTATGAGAAGAACATAATGAAGCCTGACTCAGCTAATGTCA CAACATGGTGCTACTTCTGAAGCCTGACTCAGCTAATGTCACAACATGGTGCTACTTCTT CTTCTTTTTGTTAACAGCAACGAACCCTAGAAATATATCCTGTGTACCTCACTGTCCAAT ATGAAAACCGTAAAGTGCCTTATAGGAATTTGCGTAACTAACACACCCTGCTTCATTGAC CTCTACTTGCTGAAGGAGAAAAAGACAGCGATAAGCTTCAATAGTGGCATACCAAATGGC ACTTTTGATGAAATAAAATATCAATATTTTCTGCAATCCAATGCACTGATGTGTGAAGTG AGAACTCCATCAGAAAACCAAAGGGTGCTAGGAGGTGTGGGTGCCTTCCATACTGTTTGC CCATTTTCATTCTTGTATTATAATTAATTTTCTACCCCCAGAGATAAATGTTTGTTTATA TCACTGTCTAGCTGTTTCAAAATTTAGGTCCCTTGGTCTGTACAAATAATAGCAATGTAA AAATGGTTTTTTGAACCTCCAAATGGAATTACAGACTCAGTAGCCATATCTTCCAACCCC CCAGTATAAATTTCTGTCTTTCTGCTATGTGTGGTACTTTGCAGCTGCTTTTGCAGAAAT CACAATTTTCCTGTGGAATAAAGATGGTCCAAAAATAGTCAAAAATTAAATATATATATA TATTAGTAATTTATATAGATGTCAGCAATTAGGCAGATCAAGGTTTAGTTTAACTTCCAC TGTTAAAATAAAGCTTACATAGTTTTCTTCCTTTGAAAGACTGTGCTGTCCTTTAACATA GGTTTTTAAAGACTAGGATATTGAATGTGAAACATCCGTTTTCATTGTTCACTTCTAAAC CAAAAATTATGTGTTGCCAAAACCAAACCCAGGTTCATGAATATGGTGTCTATTATAGTG AAACATGTACTTTGAGCTTATTGTTTTTATTCTGTATTAAATATTTTCAGGGTTTTAAAC ACTAATCACAAACTGAATGACTTGACTTCAAAAGCAACAACCTTAAAGGCCGTCATTTCA TTAGTATTCCTCATTCTGCATCCTAGCTTGAAAAACAGCTCTGTTGAATCACAGTATCAG TATTTTCACACGTAAGCACATTCGGGCCATTTCCGTGGTTTCTCATGAGCTGTGTTCACA GACCTCAGCAGGGCATCGCATGGACCGCAGGAGGGCAGATTCGGACCACTAGGCCTGAAA TGACATTTCACTAAAAGTCTCCAAAACATTTCTAAGACTACTAAGGCCTTTTATGTAATT TCTTTAAATGTGTATTTCTTAAGAATTCAAATTTGTAATAAAACTATTTGTAT

Genomic Sequence Description chromosome 13 working draft sequence segment, complete

Genomic Sequence

	Sequence Information

Literature

	Literature

PubMed: 10504326 Regulation of the RhoA pathway in human endothelial cell spreading on type IV collagen: role of calcium influx.
Masiero L, Lapidos KA, Ambudkar I, Kohn EC
J Cell Sci 1999 Oct;112 ( Pt 19):3205-13

PubMed: 9225741 Effects of extracellular matrix components on axonal outgrowth from peripheral nerves of adult animals in vitro.
Tonge DA, Golding JP, Edbladh M, Kroon M, Ekstrom PE, Edstrom A
Exp Neurol 1997 Jul;146(1):81-90

PubMed: 7795882 Basement membrane (type IV) collagen.
Kuhn K
Matrix Biol 1995 Feb;14(6):439-45

PubMed: 3360855 Differential effects of laminin, intact type IV collagen, and specific domains of type IV collagen on endothelial cell adhesion and migration.
Herbst TJ, McCarthy JB, Tsilibary EC, Furcht LT.
J Cell Biol. 1988 Apr;106(4):1365-73.

FAQ

PubMed: 10504326	Regulation of the RhoA pathway in human endothelial cell spreading on type IV collagen: role of calcium influx. Masiero L, Lapidos KA, Ambudkar I, Kohn EC J Cell Sci 1999 Oct;112 ( Pt 19):3205-13
PubMed: 9225741	Effects of extracellular matrix components on axonal outgrowth from peripheral nerves of adult animals in vitro. Tonge DA, Golding JP, Edbladh M, Kroon M, Ekstrom PE, Edstrom A Exp Neurol 1997 Jul;146(1):81-90
PubMed: 7795882	Basement membrane (type IV) collagen. Kuhn K Matrix Biol 1995 Feb;14(6):439-45
PubMed: 3360855	Differential effects of laminin, intact type IV collagen, and specific domains of type IV collagen on endothelial cell adhesion and migration. Herbst TJ, McCarthy JB, Tsilibary EC, Furcht LT. J Cell Biol. 1988 Apr;106(4):1365-73.