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SDC3 (Homo sapiens) in pDONR221 (Gateway donor/master vector)

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Explanation of Terms


Gene: Gene Symbol:  SDC3
Gene Name:  syndecan 3
Sequence              Map: pDONR cofig.pdf
Original Clone ID: FLH181244.01L
Keyword: None
Species: Homo sapiens
Type: cDNA
Vector Name: pDONR221               Format:  FUSION
Source: HIP
Description: None
Comments: None
Mutation/
Discrepancy :
No / No
Publications: None
Authors: HIP
HsCD00040848

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AVAILABLE
No restriction
Special MTA: None

 

Insert sequence: 1113nts         Open reading frame : 1 to 1113
Reference Sequence Alignment

ATGGCCATTGCTTACCTGGGATCCTCATGCCCCTCACAACCACCCAGCTCCCTAGCTCTC
TCCCTCTCCCCCACCCCCTCAGACTTCGAGCAGGAGTCGGGCATTGAGACAGCCATGCGC
TTCAGCCCAGATGTAGCCCTGGCGGTGTCCACCACACCATTTGAAGAGCTCCCCTCTGAG
CGCCCCACCCTGGAGCCAGCCACCAGCCCCCTGGTGGTGACAGAAGTCCCGGAAGAGCCC
AGCCAGAGAGCCACCACCGTCTCCACTACCATGGCTACCACTGCTGCCACAAGCACAGGG
GACCCGACTGTGGCCACAGTGCCTGCCACAGTGGCCACCGCCACCCCCAGCACCCCTGCA
GCACCCCCTTTTACGGCCACCACTGCTGTTATAAGGACCACTGGCGTACGGAGGCTTCTG
CCTCTCCCACTGACCACAGTGGCTACGGCACGGGCCACTACCCCCGAGGCGCCCTCCCCG
CCCACCACGGCGGCTGTCTTGGACACCGAGGCCCCAACACCCAGGCTGGTCAGCACAGCT
ACCTCCCGGCCAAGAGCCCTTCCCAGGCCGGCCACCACCCAGGAGCCTGACATCCCTGAG
AGGAGCACCCTGCCCCTGGGGACCACTGCCCCTGGACCCACAGAGGTGGCTCAGACCCCA
ACTCCAGAGACCTTCCTGACCACAATCCGGGATGAGCCAGAGGTTCCGGTGAGTGGGGGG
CCCAGTGGAGACTTCGAGCTGCCAGAAGAAGAGACCACACAACCAGACACAGCCAATGAG
GTGGTAGCTGTGGGAGGGGCTGCGGCCAAGGCATCATCTCCACCTGGGACACTGCCCAAG
GGTGCCCGCCCGGGCCCTGGCCTCCTGGACAATGCCATCGACTCGGGCAGCTCAGCTGCT
CAGCTGCCTCAGAAGAGTATCCTGGAGCGGAAGGAGGTGCTCGTAGCTGTGATTGTGGGC
GGGGTGGTGGGCGCCCTCTTTGCTGCCTTCTTGGTCACACTGCTCATCTATCGTATGAAG
AAAAAGGATGAGGGCAGCTACACGCTGGAGGAACCCAAGCAGGCGAGCGTCACATACCAG
AAGCCTGACAAGCAGGAGGAGTTCTATGCCTTG


Coding Sequence Details
Insert Sequence Verified?: Y Verification Method: Sequence Verification
Reference Sequence Annotations:
End on reference sequence 1446
Start on reference sequence 334
Mutations:
None
Discrepancy:
None
5' Linker Sequence:
5p GTACAAAAAAGCAGGCTCCACC(atg-goi)

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

 

 Recommended Growth Condition:

Distributed in bacterial strain : DH5-alpha T1 phage resistant
Antibiotic Selection: Host Type:  bacterial    Marker:  kanamycin
Bacterial Selection Condition:  50ug/mL kanamycin
Growth Condition:  Growth with the single antibiotic in LB at 37 degrees is recommended.
Comments:  Conditions for Gateway-type vectors in recombined (with insert) form and other kanamycin resistant vectors.
Protein Expression Results: None
Recommended expression in: Not Applicable
       DyNA Vector Map

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Vector Name: pDONR221

pDONR221 in advanced viewed

Synonyms: None
Sequencing Primer: Forward:  U19
Reverse:  AttP2
Description: Recombinational donor/master vector with M13 F and R primer sites; kanamycin resistance; recombinational cloning.
Comments: The position of features were determined for the unrecombined (empty) form of the vector, which is described in detail on the Invitrogen website.
Size (bp): 4762
Parent Vector: None
Empty Vector: None
Properties: Gateway, donor (entry), recombinational cloning
Author Name: Invitrogen
Publications: None
Vector Map:         Vector Sequence:
Sequence:

 



Vector Features:

Type Name Description Start Position End Position
bacterial origin ColE1 ColE1 (pUC-type) origin of replication 4086 4759
negative selection marker ccdB ccdB negative selection gene (death cassette), LOST in recombined (with insert) form 1502 1197
primer site M13 forward primer M13 Forward priming site 537 552
primer site M13 reverse primer M13 Reverse priming site 3027 3034
recombination site attP1 attP recombination site 1 LOST in recombined (with insert) form 570 801
recombination site attL1 attL recombination site 1 present in recombined (with insert) form only, position is approximate 570 801
recombination site attL2 attL recombination site 2 present in recombined (with insert) form only, position is approximate 2985 2754
recombination site attP2 attP recombination site 2 LOST in recombined (with insert) form 2985 2754
selectable marker CmR chloramphenicol resistance gene, LOST in recombined (with insert) form 2506 1847
selectable marker KanR kanamycin resistance gene 3156 3965
trxn termination sequence rrnB T2 rrnB T2 transcription termination sequence 295 268
trxn termination sequence rrnB T1 rrnB T1 transcription termination sequence 470 427

 

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

Gene

 

Gene Symbol : SDC3
Symbol Nomenclature : SDC3
SYNONYM : SDCN; SYND3
Designation : N-syndecan|syndecan neural type|syndecan proteoglycan 3|syndecan-3
Full Nomenclature : syndecan 3
GENEID : 9672
HGNC : 10660
MIM : 186357
Target GenBank: BC013974

 

Reference Sequence Alignment

  

HsCD00040848      ------------------------------------------------------------
NM_014654.3       ATGAAGCCGGGGCCGCCGCACCGTGCCGGGGCCGCCCACGGGGCCGGCGCCGGGGCCGGG
                                                                              

HsCD00040848      ------------------------------------------------------------
NM_014654.3       GCCGCGGCCGGGCCCGGGGCCCGCGGGCTGCTCCTGCCACCGCTGCTGCTGCTGCTGCTG
                                                                              

HsCD00040848      ------------------------------------------------------ATGGCC
NM_014654.3       GCGGGGCGCGCCGCGGGGGCCCAGCGCTGGCGCAGTGAGAACTTCGAGAGACCCGTGGAC
                                                                        .***.*

HsCD00040848      ATTGCTTACCTGGGATCCTCATGCCCCTCACAACCACCCAGCTCCCTAGCTCTCTCCCTC
NM_014654.3       CTGGAGGGCTCTGGGGATGATGACTCCTTTCCCGATGATGAACTGGATGACCTCTACTCG
                  .* *.  .*   **. .  .: .* *** :*.. .: . ...    ::*. ****.*   

HsCD00040848      TCCCCCACCCCCTCAGACTTCGAGCAGGAGTCGGGCATTGAGACAGCCATGCGCTTCAGC
NM_014654.3       GGGTCGGGCTCGGGCTACTTCGAGCAGGAGTCGGGCATTGAGACAGCCATGCGCTTCAGC
                      * . * *   . ********************************************

HsCD00040848      CCAGATGTAGCCCTGGCGGTGTCCACCACACCATT-------------------------
NM_014654.3       CCAGATGTAGCCCTGGCGGTGTCCACCACACCTGCGGTGCTGCCCACCACGAACATCCAG
                  ********************************:                           

HsCD00040848      -----------------TGAAGAGCTCCCCTCTGAGCGCCCCACCCTGGAGCCAGCCACC
NM_014654.3       CCTGTGGGCACACCATTTGAAGAGCTCCCCTCTGAGCGCCCCACCCTGGAGCCAGCCACC
                                   *******************************************

HsCD00040848      AGCCCCCTGGTGGTGACAGAAGTCCCGGAAGAGCCCAGCCAGAGAGCCACCACCGTCTCC
NM_014654.3       AGCCCCCTGGTGGTGACAGAAGTCCCGGAAGAGCCCAGCCAGAGAGCCACCACCGTCTCC
                  ************************************************************

HsCD00040848      ACTACCATGGCTACCACTGCTGCCACAAGCACAGGGGACCCGACTGTGGCCACAGTGCCT
NM_014654.3       ACTACCATGGCTACCACTGCTGCCACAAGCACAGGGGACCCGACTGTGGCCACAGTGCCT
                  ************************************************************

HsCD00040848      GCCACAGTGGCCACCGCCACCCCCAGCACCCCTGCAGCACCCCCTTTTACGGCCACCACT
NM_014654.3       GCCACAGTGGCCACCGCCACCCCCAGCACCCCTGCAGCACCCCCTTTTACGGCCACCACT
                  ************************************************************

HsCD00040848      GCTGTTATAAGGACCACTGGCGTACGGAGGCTTCTGCCTCTCCCACTGACCACAGTGGCT
NM_014654.3       GCTGTTATAAGGACCACTGGCGTACGGAGGCTTCTGCCTCTCCCACTGACCACAGTGGCT
                  ************************************************************

HsCD00040848      ACGGCACGGGCCACTACCCCCGAGGCGCCCTCCCCGCCCACCACGGCGGCTGTCTTGGAC
NM_014654.3       ACGGCACGGGCCACTACCCCCGAGGCGCCCTCCCCGCCCACCACGGCGGCTGTCTTGGAC
                  ************************************************************

HsCD00040848      ACCGAGGCCCCAACACCCAGGCTGGTCAGCACAGCTACCTCCCGGCCAAGAGCCCTTCCC
NM_014654.3       ACCGAGGCCCCAACACCCAGGCTGGTCAGCACAGCTACCTCCCGGCCAAGAGCCCTTCCC
                  ************************************************************

HsCD00040848      AGGCCGGCCACCACCCAGGAGCCTGACATCCCTGAGAGGAGCACCCTGCCCCTGGGGACC
NM_014654.3       AGGCCGGCCACCACCCAGGAGCCTGACATCCCTGAGAGGAGCACCCTGCCCCTGGGGACC
                  ************************************************************

HsCD00040848      ACTGCCCCTGGACCCACAGAGGTGGCTCAGACCCCAACTCCAGAGACCTTCCTGACCACA
NM_014654.3       ACTGCCCCTGGACCCACAGAGGTGGCTCAGACCCCAACTCCAGAGACCTTCCTGACCACA
                  ************************************************************

HsCD00040848      ATCCGGGATGAGCCAGAGGTTCCGGTGAGTGGGGGGCCCAGTGGAGACTTCGAGCTGCCA
NM_014654.3       ATCCGGGATGAGCCAGAGGTTCCGGTGAGTGGGGGGCCCAGTGGAGACTTCGAGCTGCCA
                  ************************************************************

HsCD00040848      GAAGAAGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTGTGGGAGGGGCTGCG
NM_014654.3       GAAGAAGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTGTGGGAGGGGCTGCG
                  ************************************************************

HsCD00040848      GCCAAGGCATCATCTCCACCTGGGACACTGCCCAAGGGTGCCCGCCCGGGCCCTGGCCTC
NM_014654.3       GCCAAGGCATCATCTCCACCTGGGACACTGCCCAAGGGTGCCCGCCCGGGCCCTGGCCTC
                  ************************************************************

HsCD00040848      CTGGACAATGCCATCGACTCGGGCAGCTCAGCTGCTCAGCTGCCTCAGAAGAGTATCCTG
NM_014654.3       CTGGACAATGCCATCGACTCGGGCAGCTCAGCTGCTCAGCTGCCTCAGAAGAGTATCCTG
                  ************************************************************

HsCD00040848      GAGCGGAAGGAGGTGCTCGTAGCTGTGATTGTGGGCGGGGTGGTGGGCGCCCTCTTTGCT
NM_014654.3       GAGCGGAAGGAGGTGCTCGTAGCTGTGATTGTGGGCGGGGTGGTGGGCGCCCTCTTTGCT
                  ************************************************************

HsCD00040848      GCCTTCTTGGTCACACTGCTCATCTATCGTATGAAGAAAAAGGATGAGGGCAGCTACACG
NM_014654.3       GCCTTCTTGGTCACACTGCTCATCTATCGTATGAAGAAAAAGGATGAGGGCAGCTACACG
                  ************************************************************

HsCD00040848      CTGGAGGAACCCAAGCAGGCGAGCGTCACATACCAGAAGCCTGACAAGCAGGAGGAGTTC
NM_014654.3       CTGGAGGAACCCAAGCAGGCGAGCGTCACATACCAGAAGCCTGACAAGCAGGAGGAGTTC
                  ************************************************************

HsCD00040848      TATGCCTTG
NM_014654.3       TATGCCTAG
                  *******:*

Pathways

NCI : Proteoglycan syndecan-mediated signaling events
NCI : Syndecan-3-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 : O75056
HPRD : 01719

Clone

Cloning Information : 181244
HIP Master Clone ID : 156188
Original Clone ID : FLH181244.01L

Organism


TAX_ID : 9606
Species Specific ID: 9672

Genome

Chromosome : 1
Map Location : 1p35.2

Reagents

Labome : SDC3-antibody