Gauge Your Current Familiarity with NCBI Resources...An Informal Pretest

Below is a sample human sequence, followed by twelve questions about it, to gauge your current familiarity with some of NCBI's bioinformatics resources. Just answer the questions you can and don't worry about the others. By the end of the module, you should be able to answer all of the questions in 10-15 minutes or less. The questions apply some key concepts and skills covered in the 3-day introductory course, which are briefly summarized in this Information Hubs module. >gi|904118 Sample human sequence for NAWBIS/InfoHubs module TGGGACAGGCAGCTCCGGGGTCCGCGGTTTCACATCGGAAACAAAACAGCGGCTGGTCTGGAAGGAACCT GAGCTACGAGCCGCGGCGGCAGCGGGGCGGCGGGGAAGCGTATACCTAATCTGGGAGCCTGCAAGTGACA ACAGCCTTTGCGGTCCTTAGACAGCTTGGCCTGGAGGAGAACACATGAAAGAAAGAACCTCAAGAGGCTT TGTTTTCTGTGAAACAGTATTTCTATACAGTTGCTCCAATGACAGAGTTACCTGCACCGTTGTCCTACTT CCAGAATGCACAGATGTCTGAGGACAACCACCTGAGCAATACTGTACGTAGCCAGAATGACAATAGAGAA CGGCAGGAGCACAACGACAGACGGAGCCTTGGCCACCCTGAGCCATTATCTAATGGACGACCCCAGGGTA ACTCCCGGCAGGTGGTGGAGCAAGATGAGGAAGAAGATGAGGAGCTGACATTGAAATATGGCGCCAAGCA TGTGATCATGCTCTTTGTCCCTGTGACTCTCTGCATGGTGGTGGTCGTGGCTACCATTAAGTCAGTCAGC TTTTATACCCGGAAGGATGGGCAGCTAATCTATACCCCATTCACAGAAGATACCGAGACTGTGGGCCAGA GAGCCCTGCACTCAATTCTGAATGCTGCCATCATGATCAGTGTCATTGTTGTCATGACTATCCTCCTGGT GGTTCTGTATAAATACAGGTGCTATAAGGTCATCCATGCCTGGCTTATTATATCATCTCTATTGTTGCTG TTCTTTTTTTCATTCATTTACTTGGGGGAAGTGTTTAAAACCTATAACGTTGCTGTGGACTACATTACTG TTGCACTCCTGATCTGGAATTTTGGTGTGGTGGGAATGATTTCCATTCACTGGAAAGGTCCACTTCGACT CCAGCAGGCATATCTCATTATGATTAGTGCCCTCATGGCCCTGGTGTTTATCAAGTACCTCCCTGAATGG ACTGCGTGGCTCATCTTGGCTGTGATTTCAGTATATGATTTAGTGGCTGTTTTGTGTCCGAAAGGTCCAC TTCGTATGCTGGTTGAAACAGCTCAGGAGAGAAATGAAACGCTTTTTCCAGCTCTCATTTACTCCTCAAC AATGGTGTGGTTGGTGAATATGGCAGAAGGAGACCCGGAAGCTCAAAGGAGAGTATCCAAAAATTCCAAG TATAATGCAGAAAGCACAGAAAGGGAGTCACAAGACACTGTTGCAGAGAATGATGATGGCGGGTTCAGTG AGGAATGGGAAGCCCAGAGGGACAGTCATCTAGGGCCTCATCGCTCTACACCTGAGTCACGAGCTGCTGT CCAGGAACTTTCCAGCAGTATCCTCGCTGGTGAAGACCCAGAGGAAAGGGGAGTAAAACTTGGATTGGGA GATTTCATTTTCTACAGTGTTCTGGTTGGTAAAGCCTCAGCAACAGCCAGTGGAGACTGGAACACAACCA TAGCCTGTTTCGTAGCCATATTAATTGGTTTGTGCCTTACATTATTACTCCTTGCCATTTTCAAGAAAGC ATTGCCAGCTCTTCCAATCTCCATCACCTTTGGGCTTGTTTTCTACTTTGCCACAGATTATCTTGTACAG CCTTTTATGGACCAATTAGCATTCCATCAATTTTATATCTAGCATATTTGCGGTTAGAATCCCATGGATG TTTCTTCTTTGACTATAACCAAATCTGGGGAGGACAAAGGTGATTTTCCTGTGTCCACATCTAACAAAGT CAAGATTCCCGGCTGGACTTTTGCAGCTTCCTTCCAAGTCTTCCTGACCACCTTGCACTATTGGACTTTG GAAGGAGGTGCCTATAGAAAACGATTTTGAACATACTTCATCGCAGTGGACTGTGTCCCTCGGTGCAGAA ACTACCAGATTTGAGGGACGAGGTCAAGGAGATATGATAGGCCCGGAAGTTGCTGTGCCCCATCAGCAGC TTGACGCGTGGTCACAGGACGATTTCACTGACACTGCGAACTCTCAGGACTACCGGTTACCAAGAGGTTA GGTGAAGTGGTTTAAACCAAACGGAACTCTTCATCTTAAACTACACGTTGAAAATCAACCCAATAATTCT GTATTAACTGAATTCTGAACTTTTCAGGAGGTACTGTGAGGAAGAGCAGGCACCAGCAGCAGAATGGGGA ATGGAGAGGTGGGCAGGGGTTCCAGCTTCCCTTTGATTTTTTGCTGCAGACTCATCCTTTTTAAATGAGA CTTGTTTTCCCCTCTCTTTGAGTCAAGTCAAATATGTAGATTGCCTTTGGCAATTCTTCTTCTCAAGCAC TGACACTCATTACCGTCTGTGATTGCCATTTCTTCCCAAGGCCAGTCTGAACCTGAGGTTGCTTTATCCT AAAAGTTTTAACCTCAGGTTCCAAATTCAGTAAATTTTGGAAACAGTACAGCTATTTCTCATCAATTCTC TATCATGTTGAAGTCAAATTTGGATTTTCCACCAAATTCTGAATTTGTAGACATACTTGTACGCTCACTT GCCCCCAGATGCCTCCTCTGTCCTCATTCTTCTCTCCCACACAAGCAGTCTTTTTCTACAGCCAGTAAGG CAGCTCTGTCRTGGTAGCAGATGGTCCCATTATTCTAGGGTCTTACTCTTTGTATGATGAAAAGAATGTG TTATGAATCGGTGCTGTCAGCCCTGCTGTCAGACCTTCTTCCACAGCAAATGAGATGTATGCCCAAAGCG GTAGAATTAAAGAAGAGTAAAATGGCTGTTGAAGC

Questions: This is the sequence data from what human gene? Did the data come from an archival (primary) or a curated (derivative) database? How can you tell? If it is archival, how can you find a curated mRNA record for this human gene, or vice versa? What is the official gene symbol? By what other gene symbols has it been known? What is the location of this gene on a cytogenetic map, and what is its bp location on the assembled human genome sequence? How many transcript variants is it known to have? On what mouse and rat chromosomes are the homologs found? What phenotypes are associated with this gene? How many allelic variants are documented in OMIM for this gene? Name a clinical laboratory in the united states that offers genetic testing for one of the phenotypes? Does NCBI offer a software tool for making a restriction map of the query sequence? How can you find out? If a user has the genomic DNA for the gene and wants to identify transcription factor binding sites, what are some databases and/or software tools that could potentially be useful? How/where did you find these? Additional (optional) questions: What conserved domains exist in the protein product? From what distributor can you obtain a clone for the full length mRNA? How can you download the genomic sequence and 3KB upstream? From what source can you obtain the genomic DNA clone for the chromosome region that contains the gene?