Manual Annotation of the human and mouse gene

Manual Annotation of the human and mouse gene index: www. allgenes. org

Allgenes. org A web interface providing access to the assembled EST and m. RNA sequences, or Do. TS RNA transcripts, contained within GUS (Genomics Unified Schema), a relational database. Computed & manual annotation has been applied to the human and mouse Do. TS RNA transcripts to associate them with their corresponding genes, creating a human and mouse gene index, Allgenes.

Do. TS RNA transcripts The assembly of sequences generates a consensus sequence or Do. TS transcript Incoming Sequences (EST/m. RNA) • Gen. Bank, db. EST sequences • Make Quality (remove vector, poly. A, NNNs) “Quality” sequences • Block with Repeat. Masker Blocked sequences • Blastn to cluster sequences “Unassembled” clusters • Assemble sequences with CAP 4 assemblies (generate consensus sequences) Dots Consensus sequences BLASTn Do. Ts consensus sequences (98% identity, 150 bps) Gene Cluster (RNA s in the Gene)

Manual Annotation efforts utilize: A web-based tool to update GUS

Annotation Tasks include: On Gene page: 1. Assigning reference RNA sequence. 2. Determining members of Gene cluster (RNA transcripts) – removing or adding members - validating RNA transcripts assigned to gene using genomic alignment, BLAST similarity and/or c. DNA clone linkages 3. Adding approved abbreviated gene name or symbol (if known) and evidence Gene description field: 4. Adding approved full gene name, aliases and evidence for them 5. Adding gene synonyms and evidence for them Gene Annotation is displayed on Gene page of allgenes. org

On RNAPage: 6. Modifying TS (RNA) description of reference sequence to reflect HUGO or MGI approved full gene name, if assigned. 7. GO Function assignment/verification – GO Function manually assigned; predicted GO Functions are verified RNA Annotation is displayed on RNA page of allgenes. org Evidence is Retrieved from GUS (e. g. , a protein domain similarity) to confirm an assignment or Evidence is added manually for the assignment (comment e. g. , source).

Proposed New Annotation Tasks: Gene level annotation - New & Old annotator tasks; underlined are tasks that are surface level annotation 1. ) Creation of gene defined exons and introns of gene – use genomic sequence definition of gene boundaries 5’ exon boundary (transcription start site) 3’ exon boundary (poly adenylation signal) 2. ) assign gene name/abbrievated gene symbol 3. ) assign full gene name (MGI or HUGO full gene name) 4. ) assign abbrievated gene synonymns 5. ) assign full gene name aliases 6. ) assign gene category (e. g. non-coding) 7. ) confirm/assign gene chromosomal location 8. ) OMIM Link assignment (verification if computationally determined)

RNA level annotation – 1. ) Define RNA transcripts from gene (create RNAs – stable sequences) ss Using exons defined by curated gene 5’ and 3’ UTRs 2. ) Assign RNA categories to created RNAs (e. g. alternative form) 3. ) Assign/confirm RNA description 4. ) Anatomy expression assignment(s) 5. ) Assign GO terms to curated RNA (non-coding RNAs, e. g. , small RNA involved in splicing)

Computational analysis on curated RNAs will be performed: Protein level annotation – 1. ) confirm/assign GO Function 2. ) confirm/assign GO Biological Process 3. ) confirm/assign GO Cellular Component 4. ) Assign protein name 5. ) Assign protein name synonyms 6. ) Assign Protein category (post translational modifications) 7. ) Protein-protein interactions assigned 8. ) Protein pathway assignments

Mouse DT. 491900 No NR protein Similarities Aligns mouse chr 5 (other cluster members with fly protein similarity) (RNA_id = 229048) Predicted protein sequence (framefinder translation) MKRKASEVKEAEANAALEEEKRRQQAELEAFENRLKGRRKKSRKRDEVAVELSPWQKYKSYLLPVCAVVV AVLMWYIFHGVD (query. Seq. ) Human DT. 426371 39% identity to 44% of (AE 003480) CG 15011 gene product [Drosophila melanogaster] (other cluster member) Aligns human chr 4 Predicted Protein Sequence (framefinder translation) MLRIKCHCKITSLYVECRKITTADVNEKNLLSCCKNQCPKELPCGHRCKEMCHPGECPFNCNQKVKLRCP CKRIKKELQCNKVRENQVSIECDTTCKEMKRKASEIKEAEAKAALEEEKRRQQAELEAFENRLKGRRKKN RKRDEVAVELSLWQKHKYYLISVCGVVVVVFAWYITHDVN GO Function Prediction for human protein is /DNA binding/transcription factor Due to Zn finger domain similarity present. This type of Zn finger is found in Drosophila shuttle craft protein, a transcription factor, which has a role in the late stages of embryonic neurogenesis. Human gene may overlap with adjacent corin gene. Score = 337 (123. 7 bits), Expect = 3. 9 e-36, P = 3. 9 e-36 Identities = 67/82 (81%), Positives = 72/82 (87%) Query: Sbjct: 1 MKRKASEVKEAEANAALEEEKRRQQAELEAFENRLKGRRKKSRKRDEVAVELSPWQKYKS 60 MKRKASE+KEAEA AALEEEKRRQQAELEAFENRLKGRRKK+RKRDEVAVELS WQK+K 99 MKRKASEIKEAEAKAALEEEKRRQQAELEAFENRLKGRRKKNRKRDEVAVELSLWQKHKY 158 61 YLLPVCAVVVAVLMWYIFHGVD 82 YL+ VC VVV V WYI H V+ 159 YLISVCGVVVVVFAWYITHDVN 180 Additional DT. Mouse DT. 60100860 100% identity to 100% of (AK 005913) putative [Mus musculus] maybe 5’ end of gene (1700012 H 24 Rik & AW 538212) sequence reversed, gap in alignment – also recent update has modified the assembly 2 sequences removed (RNA_id = 10404576)