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COL9A3 (Homo sapiens) in pDNR-Dual (Creator donor/master vector)

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Explanation of Terms


Gene: Gene Symbol:  COL9A3
Gene Name:  collagen, type IX, alpha 3
Sequence              Map: pDNR-Dual_with_human_insert.pdf
Original Clone ID: FLH141414.01L
Keyword: None
Species: Homo sapiens
Type: cDNA
Vector Name: pDNR-Dual               Format:  FUSION
Source: HIP
Description: None
Comments: None
Mutation/
Discrepancy :
No / No
Publications: PMID: 16512675
Title: Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer.
Authors: HIP
HsCD00005158

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AVAILABLE
No restriction
Special MTA: None

 

Insert sequence: 2055nts         Open reading frame : 1 to 2055
Reference Sequence Alignment

ATGGCCGGGCCGCGCGCGTGCGCCCCGCTCCTGCTCCTGCTCCTGCTCGGGGAGCTTCTG
GCGGCCGCCGGGGCGCAGAGAGTGGGACTCCCCGGCCCCCCCGGCCCCCCAGGGCCGCCC
GGGAAGCCCGGCCAGGACGGCATTGACGGAGAAGCTGGTCCTCCAGGTCTGCCTGGGCCC
CCGGGACCAAAGGGGGCCCCAGGAAAGCCGGGGAAACCAGGAGAGGCTGGGCTGCCGGGA
CTGCCGGGTGTGGATGGTCTGACTGGACGAGATGGACCCCCTGGACCCAAGGGTGCCCCT
GGGGAACGGGGAAGTCTGGGACCCCCGGGGCCGCCCGGGCTGGGGGGCAAAGGCCTCCCT
GGACCCCCCGGAGAGGCAGGAGTGAGCGGCCCCCCAGGTGGGATCGGCCTCCGCGGCCCC
CCGGGACCTTCTGGACTCCCCGGCCTCCCTGGTCCCCCAGGACCTCCCGGACCCCCTGGA
CACCCAGGAGTCCTCCCTGAAGGCGCTACTGACCTTCAGTGCCCAAGTATCTGCCCGCCA
GGTCCCCCAGGGCCCCCTGGAATGCCAGGGTTCAAGGGACCCACTGGCTACAAAGGCGAG
CAGGGGGAAGTCGGCAAGGACGGCGAGAAGGGTGACCCTGGCCCCCCTGGGCCCGCCGGC
CTCCCGGGCAGCGTGGGGCTGCAGGGCCCCCGGGGATTACGAGGACTGCCAGGGCCACTC
GGGCCCCCTGGGGACCGGGGTCCCATTGGGTTCCGAGGGCCGCCTGGGATCCCAGGAGCG
CCTGGGAAAGCGGGTGACCGAGGCGAGAGGGGCCCAGAAGGGTTCCGCGGCCCCAAGGGT
GACCTCGGCAGACCTGGTCCCAAGGGAACCCCCGGAGTGGCCGGGCCAAGCGGAGAGCCG
GGCATGCCGGGCAAGGACGGCCAGAATGGCGTGCCAGGACTCGATGGCCAGAAGGGAGAG
GCTGGTCGCAACGGTGCTCCGGGAGAGAAGGGCCCCAACGGGCTGCCGGGCCTCCCTGGA
CGAGCGGGGTCCAAAGGCGAGAAGGGAGAACGGGGCAGAGCTGGGGAGCTGGGTGAGGCC
GGCCCCTCTGGAGAGCCAGGCGTCCCTGGAGATGCTGGCATGCCTGGGGAGCGCGGTGAG
GCTGGCCACCGGGGCTCAGCGGGGGCCCTCGGCCCACAAGGCCCTCCCGGAGCCCCTGGT
GTCCGAGGCTTCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAG
GGCCTCCGAGGTGACGTGGGCGACCGGGGTCCGGGAGGTGCCGCAGGCCCTAAGGGAGAC
CAGGGTATTGCAGGTTCCGACGGTCTTCCTGGGGATAAAGGAGAACTGGGTCCCAGCGGC
CTGGTCGGACCCAAAGGAGAGTCTGGCAGTCGAGGGGAGCTGGGCCCCAAAGGCACCCAG
GGTCCCAACGGCACCAGCGGTGTTCAGGGTGTCCCCGGGCCCCCCGGTCCTCTGGGCCTG
CAGGGCGTCCCGGGTGTTCCTGGCATCACGGGGAAGCCGGGAGTTCCGGGGAAGGAGGCC
AGCGAGCAGCGCATCAGGGAGCTGTGTGGGGGGATGATCAGCGAACAAATTGCACAGTTA
GCCGCGCACCTAAGGAAGCCTTTGGCACCCGGGTCCATTGGTCGGCCCGGTCCAGCTGGC
CCCCCTGGGCCCCCAGGACCCCCAGGCTCCATTGGTCACCCTGGCGCTCGAGGACCCCCC
GGATACCGCGGTCCCACTGGGGAGCTGGGAGACCCCGGGCCCAGAGGAAACCAGGGTGAC
AGAGGAGACAAAGGCGCGGCAGGAGCAGGGCTGGACGGGCCTGAAGGAGACCAGGGGCCC
CAAGGACCCCAAGGCGTGCCCGGCACCAGCAAGGACGGCCAGGACGGTGCTCCCGGCGAG
CCTGGGCCTCCCGGAGATCCTGGGCTTCCAGGTGCCATTGGGGCCCAGGGGACACCGGGG
ATCTGCGACACCTCAGCCTGCCAAGGAGCCGTGTTAGGAGGGGTCGGGGAGAAATCAGGC
TCTCGAAGCTCATTG


Coding Sequence Details
Insert Sequence Verified?: Y Verification Method: Sequence Verification
Reference Sequence Annotations:
End on reference sequence 2067
Start on reference sequence 13
Mutations:
None
Discrepancy:
None
5' Linker Sequence:
5P GCGGCCGCATAACTTCGTATAGCATACATTATACGAAGTTATCAGTC
GACACC(ATG-GOI)

3' Linker Sequence:
5p (goi-stop)GGAAGCTTTCTAGACCATTCGTTTGGCGCGCGGGCCC

 

 Recommended Growth Condition:

Distributed in bacterial strain : DH5-alpha T1 phage resistant
Antibiotic Selection: Host Type:  bacterial    Marker:  ampicillin
Bacterial Selection Condition:  100 ug/mL ampicillin
Growth Condition:  Growth with the single antibiotic in LB at 37 degrees is recommended.
Comments:  Commonly used conditions for ampicillin resistant plasmid clones.
Protein Expression Results: None
Recommended expression in: Not Applicable
       DyNA Vector Map

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Vector Name: pDNR-Dual

pDNR-Dual in advanced viewed

Synonyms: None
Sequencing Primer: Forward:  M13F
Reverse:  Unknown
Description: Recombinational donor/master vector with 6xHN tag ORF, T7 and M13 primer sites; ampicillin resistance; restriction enzyme cloning (into) and recombinational cloning (from).
Comments: The position of features were detemined for the empty form of the vector, which is described in detail on the BD/Clontech website. Subcloning into the MCS was performed using the infusion reaction strategy and some restriction sites in the MCS may be lost after an insert is added.
Size (bp): 4938
Parent Vector: None
Empty Vector: None
Properties: Creator, donor (entry), loxP, multiple cloning site, recombinational cloning, with tag/fusion/marker
Author Name: BD Biosciences Clontech
Publications: None
Vector Map:         Vector Sequence:
Sequence:

 



Vector Features:

Type Name Description Start Position End Position
MCS MCS restriction enzyme-type multiple cloning site 45 129
bacterial origin ColE1 ColE1 (pUC-type) origin of replication 4111 4574
negative selection marker SacB SacB negative selection marker gene (sucrose sensitivity) 1057 2972
primer site M13 primer M13 primer sequencing site 4839 4855
primer site T7 primer T7 RNA Pol primer sequencing site 4865 4883
recombination site loxP site loxP recombination site 1015 1048
recombination site loxP site loxP recombination site 9 42
selectable marker CmR chloramphenicol resistance gene ORF (functional only after recombination of insert into vector with promoter) 986 327
selectable marker AmpR ampicillin resistance gene 3103 3963
splice donor site SD site splice donor site 132 136
tag HN 6xHN epitope tag 141 176

 

  • Gene
  • Pathways
  • Protein
  • Clone
  • Organism
  • Genome
  • Reagents

Gene

 

Gene Symbol : COL9A3
Symbol Nomenclature : COL9A3
SYNONYM : DJ885L7.4.1; EDM3; IDD; MED
Designation : collagen IX, alpha-3 polypeptide|collagen alpha-3(IX) chain|collagen type IX proteoglycan
Full Nomenclature : collagen, type IX, alpha 3
GENEID : 1299
Locus Tag : RP5-885L7.6
GI : 60654276
GenBank Accession : AY892914
HGNC : 2219
MIM : 120270
Vega : OTTHUMG00000032938
Target GenBank: BC011705

 

Reference Sequence Alignment

  

HsCD00005158      ATGGCCGGGCCGCGCGCGTGCGCCCCGCTCCTGCTCCTGCTCCTGCTCGGGGAGCTTCTG
NM_001853.3       ATGGCCGGGCCGCGCGCGTGCGCCCCGCTCCTGCTCCTGCTCCTGCTCGGGGAGCTTCTG
                  ************************************************************

HsCD00005158      GCGGCCGCCGGGGCGCAGAGAGTGGGACTCCCCGGCCCCCCCGGCCCCCCAGGGCCGCCC
NM_001853.3       GCGGCCGCCGGGGCGCAGAGAGTGGGACTCCCCGGCCCCCCCGGCCCCCCAGGGCCGCCC
                  ************************************************************

HsCD00005158      GGGAAGCCCGGCCAGGACGGCATTGACGGAGAAGCTGGTCCTCCAGGTCTGCCTGGGCCC
NM_001853.3       GGGAAGCCCGGCCAGGACGGCATTGACGGAGAAGCTGGTCCTCCAGGTCTGCCTGGGCCC
                  ************************************************************

HsCD00005158      CCGGGACCAAAGGGGGCCCCAGGAAAGCCGGGGAAACCAGGAGAGGCTGGGCTGCCGGGA
NM_001853.3       CCGGGACCAAAGGGGGCCCCAGGAAAGCCGGGGAAACCAGGAGAGGCTGGGCTGCCGGGA
                  ************************************************************

HsCD00005158      CTGCCGGGTGTGGATGGTCTGACTGGACGAGATGGACCCCCTGGACCCAAGGGTGCCCCT
NM_001853.3       CTGCCGGGTGTGGATGGTCTGACTGGACGAGATGGACCCCCTGGACCCAAGGGTGCCCCT
                  ************************************************************

HsCD00005158      GGGGAACGGGGAAGTCTGGGACCCCCGGGGCCGCCCGGGCTGGGGGGCAAAGGCCTCCCT
NM_001853.3       GGGGAACGGGGAAGTCTGGGACCCCCGGGGCCGCCCGGGCTGGGGGGCAAAGGCCTCCCT
                  ************************************************************

HsCD00005158      GGACCCCCCGGAGAGGCAGGAGTGAGCGGCCCCCCAGGTGGGATCGGCCTCCGCGGCCCC
NM_001853.3       GGACCCCCCGGAGAGGCAGGAGTGAGCGGCCCCCCAGGTGGGATCGGCCTCCGCGGCCCC
                  ************************************************************

HsCD00005158      CCGGGACCTTCTGGACTCCCCGGCCTCCCTGGTCCCCCAGGACCTCCCGGACCCCCTGGA
NM_001853.3       CCGGGACCTTCTGGACTCCCCGGCCTCCCTGGTCCCCCAGGACCTCCCGGACCCCCTGGA
                  ************************************************************

HsCD00005158      CACCCAGGAGTCCTCCCTGAAGGCGCTACTGACCTTCAGTGCCCAAGTATCTGCCCGCCA
NM_001853.3       CACCCAGGAGTCCTCCCTGAAGGCGCTACTGACCTTCAGTGCCCAAGTATCTGCCCGCCA
                  ************************************************************

HsCD00005158      GGTCCCCCAGGGCCCCCTGGAATGCCAGGGTTCAAGGGACCCACTGGCTACAAAGGCGAG
NM_001853.3       GGTCCCCCAGGGCCCCCTGGAATGCCAGGGTTCAAGGGACCCACTGGCTACAAAGGCGAG
                  ************************************************************

HsCD00005158      CAGGGGGAAGTCGGCAAGGACGGCGAGAAGGGTGACCCTGGCCCCCCTGGGCCCGCCGGC
NM_001853.3       CAGGGGGAAGTCGGCAAGGACGGCGAGAAGGGTGACCCTGGCCCCCCTGGGCCCGCCGGC
                  ************************************************************

HsCD00005158      CTCCCGGGCAGCGTGGGGCTGCAGGGCCCCCGGGGATTACGAGGACTGCCAGGGCCACTC
NM_001853.3       CTCCCGGGCAGCGTGGGGCTGCAGGGCCCCCGGGGATTACGAGGACTGCCAGGGCCACTC
                  ************************************************************

HsCD00005158      GGGCCCCCTGGGGACCGGGGTCCCATTGGGTTCCGAGGGCCGCCTGGGATCCCAGGAGCG
NM_001853.3       GGGCCCCCTGGGGACCGGGGTCCCATTGGGTTCCGAGGGCCGCCTGGGATCCCAGGAGCG
                  ************************************************************

HsCD00005158      CCTGGGAAAGCGGGTGACCGAGGCGAGAGGGGCCCAGAAGGGTTCCGCGGCCCCAAGGGT
NM_001853.3       CCTGGGAAAGCGGGTGACCGAGGCGAGAGGGGCCCAGAAGGGTTCCGCGGCCCCAAGGGT
                  ************************************************************

HsCD00005158      GACCTCGGCAGACCTGGTCCCAAGGGAACCCCCGGAGTGGCCGGGCCAAGCGGAGAGCCG
NM_001853.3       GACCTCGGCAGACCTGGTCCCAAGGGAACCCCCGGAGTGGCCGGGCCAAGCGGAGAGCCG
                  ************************************************************

HsCD00005158      GGCATGCCGGGCAAGGACGGCCAGAATGGCGTGCCAGGACTCGATGGCCAGAAGGGAGAG
NM_001853.3       GGCATGCCGGGCAAGGACGGCCAGAATGGCGTGCCAGGACTCGATGGCCAGAAGGGAGAG
                  ************************************************************

HsCD00005158      GCTGGTCGCAACGGTGCTCCGGGAGAGAAGGGCCCCAACGGGCTGCCGGGCCTCCCTGGA
NM_001853.3       GCTGGTCGCAACGGTGCTCCGGGAGAGAAGGGCCCCAACGGGCTGCCGGGCCTCCCTGGA
                  ************************************************************

HsCD00005158      CGAGCGGGGTCCAAAGGCGAGAAGGGAGAACGGGGCAGAGCTGGGGAGCTGGGTGAGGCC
NM_001853.3       CGAGCGGGGTCCAAAGGCGAGAAGGGAGAACGGGGCAGAGCTGGGGAGCTGGGTGAGGCC
                  ************************************************************

HsCD00005158      GGCCCCTCTGGAGAGCCAGGCGTCCCTGGAGATGCTGGCATGCCTGGGGAGCGCGGTGAG
NM_001853.3       GGCCCCTCTGGAGAGCCAGGCGTCCCTGGAGATGCTGGCATGCCTGGGGAGCGCGGTGAG
                  ************************************************************

HsCD00005158      GCTGGCCACCGGGGCTCAGCGGGGGCCCTCGGCCCACAAGGCCCTCCCGGAGCCCCTGGT
NM_001853.3       GCTGGCCACCGGGGCTCAGCGGGGGCCCTCGGCCCACAAGGCCCTCCCGGAGCCCCTGGT
                  ************************************************************

HsCD00005158      GTCCGAGGCTTCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAG
NM_001853.3       GTCCGAGGCTTCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAG
                  ************************************************************

HsCD00005158      GGCCTCCGAGGTGACGTGGGCGACCGGGGTCCGGGAGGTGCCGCAGGCCCTAAGGGAGAC
NM_001853.3       GGCCTCCGAGGTGACGTGGGCGACCGGGGTCCGGGAGGTGCCGCAGGCCCTAAGGGAGAC
                  ************************************************************

HsCD00005158      CAGGGTATTGCAGGTTCCGACGGTCTTCCTGGGGATAAAGGAGAACTGGGTCCCAGCGGC
NM_001853.3       CAGGGTATTGCAGGTTCCGACGGTCTTCCTGGGGATAAAGGAGAACTGGGTCCCAGCGGC
                  ************************************************************

HsCD00005158      CTGGTCGGACCCAAAGGAGAGTCTGGCAGTCGAGGGGAGCTGGGCCCCAAAGGCACCCAG
NM_001853.3       CTGGTCGGACCCAAAGGAGAGTCTGGCAGTCGAGGGGAGCTGGGCCCCAAAGGCACCCAG
                  ************************************************************

HsCD00005158      GGTCCCAACGGCACCAGCGGTGTTCAGGGTGTCCCCGGGCCCCCCGGTCCTCTGGGCCTG
NM_001853.3       GGTCCCAACGGCACCAGCGGTGTTCAGGGTGTCCCCGGGCCCCCCGGTCCTCTGGGCCTG
                  ************************************************************

HsCD00005158      CAGGGCGTCCCGGGTGTTCCTGGCATCACGGGGAAGCCGGGAGTTCCGGGGAAGGAGGCC
NM_001853.3       CAGGGCGTCCCGGGTGTTCCTGGCATCACGGGGAAGCCGGGAGTTCCGGGGAAGGAGGCC
                  ************************************************************

HsCD00005158      AGCGAGCAGCGCATCAGGGAGCTGTGTGGGGGGATGATCAGCGAACAAATTGCACAGTTA
NM_001853.3       AGCGAGCAGCGCATCAGGGAGCTGTGTGGGGGGATGATCAGCGAACAAATTGCACAGTTA
                  ************************************************************

HsCD00005158      GCCGCGCACCTAAGGAAGCCTTTGGCACCCGGGTCCATTGGTCGGCCCGGTCCAGCTGGC
NM_001853.3       GCCGCGCACCTAAGGAAGCCTTTGGCACCCGGGTCCATTGGTCGGCCCGGTCCAGCTGGC
                  ************************************************************

HsCD00005158      CCCCCTGGGCCCCCAGGACCCCCAGGCTCCATTGGTCACCCTGGCGCTCGAGGACCCCCC
NM_001853.3       CCCCCTGGGCCCCCAGGACCCCCAGGCTCCATTGGTCACCCTGGCGCTCGAGGACCCCCT
                  *********************************************************** 

HsCD00005158      GGATACCGCGGTCCCACTGGGGAGCTGGGAGACCCCGGGCCCAGAGGAAACCAGGGTGAC
NM_001853.3       GGATACCGCGGTCCCACTGGGGAGCTGGGAGACCCCGGGCCCAGAGGAAACCAGGGTGAC
                  ************************************************************

HsCD00005158      AGAGGAGACAAAGGCGCGGCAGGAGCAGGGCTGGACGGGCCTGAAGGAGACCAGGGGCCC
NM_001853.3       AGAGGAGACAAAGGCGCGGCAGGAGCAGGGCTGGACGGGCCTGAAGGAGACCAGGGGCCC
                  ************************************************************

HsCD00005158      CAAGGACCCCAAGGCGTGCCCGGCACCAGCAAGGACGGCCAGGACGGTGCTCCCGGCGAG
NM_001853.3       CAAGGACCCCAAGGCGTGCCCGGCACCAGCAAGGACGGCCAGGACGGTGCTCCCGGCGAG
                  ************************************************************

HsCD00005158      CCTGGGCCTCCCGGAGATCCTGGGCTTCCAGGTGCCATTGGGGCCCAGGGGACACCGGGG
NM_001853.3       CCTGGGCCTCCCGGAGATCCTGGGCTTCCAGGTGCCATTGGGGCCCAGGGGACACCGGGG
                  ************************************************************

HsCD00005158      ATCTGCGACACCTCAGCCTGCCAAGGAGCCGTGTTAGGAGGGGTCGGGGAGAAATCAGGC
NM_001853.3       ATCTGCGACACCTCAGCCTGCCAAGGAGCCGTGTTAGGAGGGGTCGGGGAGAAATCAGGC
                  ************************************************************

HsCD00005158      TCTCGAAGCTCATTG
NM_001853.3       TCTCGAAGCTCATAA
                  *************:.

Pathways

NCI : Integrins in angiogenesis
NCI : Syndecan-1-mediated signaling events
Panther : Integrin signalling pathway
Reactome : Axon guidance
Reactome : Collagen biosynthesis and modifying enzymes
Reactome : Collagen degradation
Reactome : Collagen formation
Reactome : Degradation of the extracellular matrix
Reactome : Developmental Biology
Reactome : ECM proteoglycans
Reactome : Extracellular matrix organization
Reactome : Integrin cell surface interactions
Reactome : NCAM signaling for neurite out-growth
Reactome : NCAM1 interactions
Reactome : Signal Transduction
Reactome : Signaling by PDGF

Protein

UniProt : Q14050
HPRD : 00374

Clone

Cloning Information : 141414
HIP Master Clone ID : 117681
Original Clone ID : FLH141414.01L

Organism


TAX_ID : 9606
Species Specific ID: 1299

Genome

Chromosome : 20
Map Location : 20q13.3
Ensembl : ENSG00000092758

Reagents

Labome : COL9A3-antibody