A PHD1 tSaf5 326 KLDKEDDEDESDIS-ETQKECNWEKCKKKNKSDPEDILVCKNCNKSFHAECCDPPLEK-GIVSKYDWFCTECKLCIACNK hDPF3 246 HRP-QKGPDGTVIPNNYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECKSCILCGT.

Slides:

Advertisements

Similar presentations

From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd.

Advertisements

Homework Assignments due next session 1.Find a entry of interest in OMIM ( )

ATGGCAAAAGATCGTCGCAGTAATGAAGCTGAAAATATCGCTGTTGTTGAAAAACCGCTGAAATCGGACCG CTTCTTTA TCTCTGATGGTCTGCCGAGTCCGTTCGGCCCGACCGTTCGTGATGACGGTGTGAATTTTTCTGTTTATAGT.

Multiple Sequence Alignments  Assemble DNA sequences into a ‘contig’  Identify conserved residues and domains.

Biological Databases Biology outside the lab. Why do we need Bioinfomatics? Over the past few decades, major advances in the field of molecular biology,

PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1.

Aidan Budd, EMBL Heidelberg Multiple Sequence Alignments.

Supplemental Fig. S1 A B AtMYBS aa AtMYBS

C acaatataATGGAGCGTGAGACTTCGTCATCTTCAACTCCTCCGGAGGATCTTGTTACATCGATGATCGGAAAGTTCGTCGCTGTCATGTCTA b acaatataATGGAGCGTGAGACTTCGTCATCTTCAACTCCTCCGGAGGATCTTGTTACATCGATGATCGGAAAGTTCGTCGCTGTCTTGTCTA.

MAKRLVLFATVVIALVALTVAEGEASRQLQCERELQESSLEACRLVVDQQLAGRLPWSTGLQMRCCQQLRDISAKCRPVAVSQVARQYGQ MAKRLVLFATVVIGLVALTVAEGEASRQLQCERELQESSLEACRLVVDQQLAGRLPWSTGLQMRCCQQLRDISAKCRPVAVSQVARQYGQ.

Figure 8. Subcellular localisation of murine and human nuclear forms in fusion with EGFP in NIH 3T3 and HeLa cells. Ung2EGFP in NIH 3T3 (A) and HeLa (B)

22 kDa a-coixin gene cluster

Figure 1. Structure of the fly LGR2 gene and the corresponding cDNA sequence. A, Derivation of the fly LGR2 full-length cDNA from the genomic sequence.

Gene Mutations.

Volume 6, Issue 4, Pages (October 2000)

Mark M Metzstein, H.Robert Horvitz Molecular Cell

Hair Keratin Associated Proteins: Characterization of a Second High Sulfur KAP Gene Domain on Human Chromosome 211 Michael A. Rogers, Hermelita Winter,

There are four levels of structure in proteins

Volume 126, Issue 1, Pages (January 2004)

Multiple sequence alignment of S

Volume 14, Issue 5, Pages (March 2004)

A Hypervariable Invertebrate Allodeterminant

Bacterial genomics: The controlled chaos of shifty pathogens

Schematic illustration of the Bean dwarf mosaic virus (BDMV) DNA-A and DNA-B Components Used in Genome Size-Reversion Studies.(A) Linear maps are shown.

Quiz#4 LC710 11/14/11 name___________

(A) Microplate reader analysis of all eight Snf4-Kis1 BiFC combinations. (A) Microplate reader analysis of all eight Snf4-Kis1 BiFC combinations. Quantitative.

A Novel Gene Causing a Mendelian Audiogenic Mouse Epilepsy

Analysis of Telomerase Processivity

Volume 113, Issue 5, Pages (May 2003)

The Translational Landscape of the Mammalian Cell Cycle

Volume 117, Issue 3, Pages (September 1999)

Volume 64, Issue 4, Pages (October 2003)

Figure 1: The full-length cDNA and deduced amino acid sequences of Lysozyme C and amino acid sequences from rock bream, Oplegnathus fasciatus. The primers.

Sightless has homology to transmembrane acyltransferases and is required to generate active Hedgehog protein Jeffrey D. Lee, Jessica E. Treisman Current.

Warthog and Groundhog, novel families related to Hedgehog

Supplemental Figure 3 A B C T-DNA 1 2 RGLG1 2329bp 3 T-DNA 1 2 RGLG2

Antigenic Variation in Malaria

Characterization of two novel gene cassettes, dfrA27 and aadA16, in a non-O1, non- O139 Vibrio cholerae isolate from China J. Sun, M. Zhou, Q. Wu, Y.

RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System

Diabetes Mutations Delineate an Atypical POU Domain in HNF-1α

Targeted disruption of the mouse Pex14 gene.

Multiple sequence alignment & Phylogenetics Analysis

lin-35 and lin-53, Two Genes that Antagonize a C

Sean D. Taverna, Robert S. Coyne, C.David Allis Cell

Volume 11, Issue 19, Pages (October 2001)

Volume 88, Issue 2, Pages (January 1997)

Sadaf Naz, Chantal M. Giguere, David C. Kohrman, Kristina L

Michael A. Rogers, Hermelita Winter, Christian Wolf, Jürgen Schweizer

Volume 6, Issue 4, Pages (April 1996)

Cell Signalling: Receptor orphans find a family

Deletion of PREPL, a Gene Encoding a Putative Serine Oligopeptidase, in Patients with Hypotonia-Cystinuria Syndrome Jaak Jaeken, Kevin Martens, Inge.

Mutagenesis through Cas9/sgRNA-induced HDR

Analysis of GFP expression in gfp loss-of-function mutants.

Multiple Developmental Stage–Specific Enhancers Regulate CD8 Expression in Developing Thymocytes and in Thymus-Independent T Cells Wilfried Ellmeier,

Bioinformatics analysis of the small TbTim amino acid sequences.

Characterization and Mutation Analysis of Human LEFTY A and LEFTY B, Homologues of Murine Genes Implicated in Left-Right Axis Development K. Kosaki,

Identification of the GCS1 ortholog in Gonium pectorale.

Tagging of the endogenous Py03652 gene with the gfp gene in Plasmodium yoelii. Tagging of the endogenous Py03652 gene with the gfp gene in Plasmodium yoelii.

Volume 94, Issue 2, Pages (July 1998)

Shifty Ciliates Lawrence A. Klobutcher, Philip J. Farabaugh Cell

Multiple sequence alignment of STAT6 and other STAT proteins produced by ClusterW and ESpript (espript.ibcp.fr/ESPript/ESPript/). Multiple sequence alignment.

PfSec13 is a structural homolog of ScSec13·Nup145C.

Fig. 4. Targeted disruption of STK35 transcripts in mouse.

Figure 1. An outline of the novel ∼3

Mutations in NEXN, a Z-Disc Gene, Are Associated with Hypertrophic Cardiomyopathy Hu Wang, Zhaohui Li, Jizheng Wang, Kai Sun, Qiqiong Cui, Lei Song, Yubao.

Figure 1a. Insertion of sequence into Claudi capsid gene

Volume 88, Issue 6, Pages (March 1997)

Volume 97, Issue 6, Pages (June 1999)

S. moellendorffii BBI3 Is Predicted to Be a BBI Based on Sequence Similarity at the Inhibitory Motifs and Shared Primary Protein Architecture. S. moellendorffii.

Control of B Cell Production by the Adaptor Protein Lnk

Presentation transcript:

A PHD1 tSaf5 326 KLDKEDDEDESDIS-ETQKECNWEKCKKKNKSDPEDILVCKNCNKSFHAECCDPPLEK-GIVSKYDWFCTECKLCIACNK hDPF3 246 HRP-QKGPDGTVIPNNYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECKSCILCGT hBAF45a 364 SKS-VPGYKPKVIPNAICGICLKGKESNK-KGKAESLIHCSQCENSGHPSCLDMTMELVSMIKTYPWQCMECKTCIICGQ mBAF45A 363 SKS-APGYKPKVIPNALCGICLKGKESNK-KGKAESLIHCSQCDNSGHPSCLDMTMELVSMIKTYPWQCMECKTCIICGQ tSaf5 404 NTKENELLMCDCCDRPFHMSCLEPARTDIPEGRWFCKDCEKCPCCGVLLFQNYSRELLKQYSKQQVDNKIICKDCWVYYQ…549 hDPF3 325 SENDDQLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKEKASAFGCQA--------------------------…378 hBAF45a 442 PHHEEEMMFCDMCDRGYHTFCVGL--GAIPSGRWICDCCQRAPPTPR-KVGRRGKNSKEG--------------------…498 mBAF45A 441 PHHEEEMMFCDVCDRGYHTFCVGL--GAIPSGRWICDCCQRAPPTPR-KVGRRGKNSKEG--------------------…497 PHD2 B * tSaf5 KpnI XhoI * NotI SacI NEO FZZ UTR tSaf5 Saf5: A. Tetrahymena TTHERM_00241840 (tSaf5) shows homology to human (hBAF45a and hDPF3), and mice (mBAF45a) PHD domains. The two PHD domains of Saf5 are highly similar to each other (E-value 3e-14) as well as with the PHD domains of mBAF45a and hBAF45a (E-value 7e-14). The Saf5 PHD domains also share an E-value of 2e-15 with respect to the PHD domains of DPF3. The 4 proteins present 2 PHD domains in Tandem (PHD1 and PHD2). Clustal Omega Multiple Sequence Alignment from EMBL-EBI, BoxShade from ExPASy and SMART from EMBL-HEIDELBERG were used for this figure. The start and end of the bromodomains are as follows: Saf5, PHD1:344-396 PHD2:397-443; hBAF45a, PHD1:379-434 PHD2:435-479; hDPF3, PHD1:261-317 PHD2:318-364; mBAF45a, PHD1:378-433 PHD2:434-478 (SMART). Absolutely conserved residues are represented by a black shade and conserved residues are represented by a grey shade (BoxShade). The last number of last line represents the last residue for the each given sequence. B. Saf5 Cloning Strategy. The top panel represents the full gene in the MAC, the bottom panel represents the tagging cassette. The pointed lines represent where DNA replacement occurs. Arrows represent the used primers (Additional File 4). Black boxes are not coding sequences. White boxes are coding sequences. Bended arrow represents the starting codon and * represents the stop codons.