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SDC4 (Homo sapiens) in pJP1520 (retroviral expression vector)

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Explanation of Terms


Gene: Gene Symbol:  SDC4
Gene Name:  syndecan 4
Sequence             
Original Clone ID: FLH213713.01X
Keyword: None
Species: Homo sapiens
Type: cDNA
Vector Name: pJP1520               Format:  CLOSED
Source: HIP
Description: None
Comments: None
Mutation/
Discrepancy :
No / No
Publications: None
Authors:
HsCD00074146

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AVAILABLE
No restriction
Special MTA: None

 

Insert sequence: 597nts         Open reading frame : 1 to 597
Reference Sequence Alignment

ATGGCCCCCGCCCGTCTGTTCGCGCTGCTGCTGTTCTTCGTAGGCGGAGTCGCCGAGTCG
ATCCGAGAGACTGAGGTCATCGACCCCCAGGACCTCCTAGAAGGCCGATACTTCTCCGGA
GCCCTACCAGACGATGAGGATGTAGTGGGGCCCGGGCAGGAATCTGATGACTTTGAGCTG
TCTGGCTCTGGAGATCTGGATGACTTGGAAGACTCCATGATCGGCCCTGAAGTTGTCCAT
CCCTTGGTGCCTCTAGATAACCATATCCCTGAGAGGGCAGGGTCTGGGAGCCAAGTCCCC
ACCGAACCCAAGAAACTAGAGGAGAATGAGGTTATCCCCAAGAGAATCTCACCCGTTGAA
GAGAGTGAGGATGTGTCCAACAAGGTGTCAATGTCCAGCACTGTGCAGGGCAGCAACATC
TTTGAGAGAACGGAGGTCCTGGCAGCTCTGATTGTGGGTGGCATCGTGGGCATCCTCTTT
GCCGTCTTCCTGATCCTACTGCTCATGTACCGTATGAAGAAGAAGGATGAAGGCAGCTAT
GACCTGGGCAAGAAACCCATCTACAAGAAAGCCCCCACCAATGAGTTCTACGCGTAG


Coding Sequence Details
Insert Sequence Verified?: Y Verification Method: Insert was fully sequenced in parent vector; Verification by restriction enzyme digest
Reference Sequence Annotations:
End on reference sequence 637
Start on reference sequence 41
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
Host Type:  bacterial    Marker:  chloramphenicol
Host Type:  mammalian    Marker:  puromycin
Bacterial Selection Condition:  100 ug/mL ampicillin, 34 ug/mL chloramphenicol
Growth Condition:  Growth with the double antibiotic in LB supplemented with 7% sucrose at 37 degrees is recommended.
Comments:  Conditions for Creator-type vectors in with insert (recombined) form. Selection differs for the unrecombined, empty form of the vectors.
Protein Expression Results: None
Recommended expression in: Not Applicable
       DyNA Vector Map

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Vector Name: pJP1520

pJP1520 in advanced viewed

Synonyms: None
Sequencing Primer: Forward:  JPO113
Reverse:  Unknown
Description: Retroviral expression vector with CMV promoter, MMV-type 5p and 3p LTRs; amp resistance (puromycin for mammalian selection); recombinational cloning.
Comments: One in a series of pJP# vectors that includes puroR, blastR, hygR vectors made by J. Pearlberg at HIP
Size (bp): 7894
Parent Vector: None
Empty Vector: None
Properties: Creator, acceptor (destination), loxP, mammalian expression, mammalian transduction, retroviral vector
Author Name: Ed Harlow
Joseph Pearlberg
Publications: None
Vector Map:         Vector Sequence:
Sequence:

 



Vector Features:

Type Name Description Start Position End Position
bacterial origin ori bacterial origin of replication 5659 6341
gene fragment gag/pol/env non-functional gag/pol/env for packaging efficiency 1871 2644
primer JPO113 forward sequencing primer: GCGGTTTTGGCAGTACATCAATGGGCG 3555 3581
primer site PBSQ primer binding sequence (glutamine tRNA primer binding site) 1140 1156
promoter bacterial bacterial promoter (for chlR ORF in Creator-type inserts) 3879 4005
recombination site LoxP LoxP site for recombinational cloning 3651 3684
selectable marker AmpR ampicillin resistance gene (beta-lactamase) 6237 7094
viral LTR 5p LTR 5p viral LTR (MPSV U3, R, U5) 550 1139
viral LTR 3p LTR 3p viral LTR (MPSV U3, R, U5) 3962 4551

 

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

Gene

 

Gene Symbol : SDC4
Symbol Nomenclature : SDC4
SYNONYM : SYND4
Designation : amphiglycan|ryudocan amphiglycan|ryudocan core protein|syndecan 4 (amphiglycan, ryudocan)|syndecan proteoglycan 4|syndecan-4
Full Nomenclature : syndecan 4
GENEID : 6385
HGNC : 10661
MIM : 600017
Vega : OTTHUMG00000033083
Target GenBank: BC030805

 

Reference Sequence Alignment

  

HsCD00074146      ATGGCCCCCGCCCGTCTGTTCGCGCTGCTGCTGTTCTTCGTAGGCGGAGTCGCCGAGTCG
NM_002999.3       ATGGCCCCCGCCCGTCTGTTCGCGCTGCTGCTGTTCTTCGTAGGCGGAGTCGCCGAGTCG
                  ************************************************************

HsCD00074146      ATCCGAGAGACTGAGGTCATCGACCCCCAGGACCTCCTAGAAGGCCGATACTTCTCCGGA
NM_002999.3       ATCCGAGAGACTGAGGTCATCGACCCCCAGGACCTCCTAGAAGGCCGATACTTCTCCGGA
                  ************************************************************

HsCD00074146      GCCCTACCAGACGATGAGGATGTAGTGGGGCCCGGGCAGGAATCTGATGACTTTGAGCTG
NM_002999.3       GCCCTACCAGACGATGAGGATGTAGTGGGGCCCGGGCAGGAATCTGATGACTTTGAGCTG
                  ************************************************************

HsCD00074146      TCTGGCTCTGGAGATCTGGATGACTTGGAAGACTCCATGATCGGCCCTGAAGTTGTCCAT
NM_002999.3       TCTGGCTCTGGAGATCTGGATGACTTGGAAGACTCCATGATCGGCCCTGAAGTTGTCCAT
                  ************************************************************

HsCD00074146      CCCTTGGTGCCTCTAGATAACCATATCCCTGAGAGGGCAGGGTCTGGGAGCCAAGTCCCC
NM_002999.3       CCCTTGGTGCCTCTAGATAACCATATCCCTGAGAGGGCAGGGTCTGGGAGCCAAGTCCCC
                  ************************************************************

HsCD00074146      ACCGAACCCAAGAAACTAGAGGAGAATGAGGTTATCCCCAAGAGAATCTCACCCGTTGAA
NM_002999.3       ACCGAACCCAAGAAACTAGAGGAGAATGAGGTTATCCCCAAGAGAATCTCACCCGTTGAA
                  ************************************************************

HsCD00074146      GAGAGTGAGGATGTGTCCAACAAGGTGTCAATGTCCAGCACTGTGCAGGGCAGCAACATC
NM_002999.3       GAGAGTGAGGATGTGTCCAACAAGGTGTCAATGTCCAGCACTGTGCAGGGCAGCAACATC
                  ************************************************************

HsCD00074146      TTTGAGAGAACGGAGGTCCTGGCAGCTCTGATTGTGGGTGGCATCGTGGGCATCCTCTTT
NM_002999.3       TTTGAGAGAACGGAGGTCCTGGCAGCTCTGATTGTGGGTGGCATCGTGGGCATCCTCTTT
                  ************************************************************

HsCD00074146      GCCGTCTTCCTGATCCTACTGCTCATGTACCGTATGAAGAAGAAGGATGAAGGCAGCTAT
NM_002999.3       GCCGTCTTCCTGATCCTACTGCTCATGTACCGTATGAAGAAGAAGGATGAAGGCAGCTAT
                  ************************************************************

HsCD00074146      GACCTGGGCAAGAAACCCATCTACAAGAAAGCCCCCACCAATGAGTTCTACGCGTAG
NM_002999.3       GACCTGGGCAAGAAACCCATCTACAAGAAAGCCCCCACCAATGAGTTCTACGCGTGA
                  *******************************************************..

Pathways

NCI : Beta3 integrin cell surface interactions
NCI : FGF signaling pathway
NCI : Proteoglycan syndecan-mediated signaling events
NCI : Syndecan-4-mediated signaling events
Reactome : A tetrasaccharide linker sequence is required for GAG synthesis
Reactome : Chondroitin sulfate/dermatan sulfate metabolism
Reactome : Disease
Reactome : Diseases associated with visual transduction
Reactome : Extracellular matrix organization
Reactome : Glycogen storage diseases
Reactome : Glycosaminoglycan metabolism
Reactome : HS-GAG biosynthesis
Reactome : HS-GAG degradation
Reactome : Heparan sulfate/heparin (HS-GAG) metabolism
Reactome : MPS I - Hurler syndrome
Reactome : MPS II - Hunter syndrome
Reactome : MPS IIIA - Sanfilippo syndrome A
Reactome : MPS IIIB - Sanfilippo syndrome B
Reactome : MPS IIIC - Sanfilippo syndrome C
Reactome : MPS IIID - Sanfilippo syndrome D
Reactome : MPS IV - Morquio syndrome A
Reactome : MPS IV - Morquio syndrome B
Reactome : MPS IX - Natowicz syndrome
Reactome : MPS VI - Maroteaux-Lamy syndrome
Reactome : MPS VII - Sly syndrome
Reactome : Metabolism
Reactome : Metabolism of carbohydrates
Reactome : Mucopolysaccharidoses
Reactome : Myoclonic epilepsy of Lafora
Reactome : Non-integrin membrane-ECM interactions
Reactome : Retinoid metabolism and transport
Reactome : Signal Transduction
Reactome : Syndecan interactions
Reactome : Visual phototransduction

Protein

SMART domain : 4.1m : putative band 4.1 homologues binding motif
UniProt : Q6FGN3
UniProt : P31431
HPRD : 08366

Clone

Cloning Information : 213713
HIP Master Clone ID : 117633
Original Clone ID : FLH213713.01X

Organism


TAX_ID : 9606
Species Specific ID: 6385

Genome

Chromosome : 20
Map Location : 20q12
Ensembl : ENSG00000124145

Reagents

Labome : SDC4-antibody