diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java b/java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java
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index 000000000..10f2bd333
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+++ b/java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java
@@ -0,0 +1,98 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.StingException;
+
+/** Holds a single transcript annotation: refseq id, gene name, genomic locations of the locus, of the coding region 
+ * and of all the exons. 
+ */
+class Transcript {
+		private String transcript_id;
+		private int strand;
+		private GenomeLoc transcript_interval;
+		private GenomeLoc transcript_coding_interval;
+		private List<GenomeLoc> exons;
+		private String gene_name;
+		private List<Integer> exon_frames;
+
+		public Transcript() {}
+		
+		public Transcript(String line) {
+			parseLine(line);
+		}
+		
+		/** Returns id of the transcript (RefSeq NM_* id) */
+		public String getTranscriptId() { return transcript_id; }
+		/** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
+		public int getStrand() { return strand; }
+		/** Returns transcript's full genomic interval (includes all exons with UTRs) */  
+		public GenomeLoc getLocation() { return transcript_interval; }
+		/** Returns genomic interval of the coding sequence (does not include UTRs, but still includes introns, since it's a single interval on the DNA) */  
+		public GenomeLoc getCodingLocation() { return transcript_coding_interval; }
+		/** Name of the gene this transcript corresponds to (NOT gene id such as Entrez etc) */
+		public String getGeneName() { return gene_name; }
+		/** Number of exons in this transcript */
+		public int getNumExons() { return exons.size(); }
+		/** Genomic location of the n-th exon; throws an exception if n is out of bounds */
+		public GenomeLoc getExonLocation(int n) {
+			if ( n >= exons.size() || n < 0 ) throw new StingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
+			return exons.get(n);
+		}
+		/** Returns the list of all exons in this transcript, as genomic intervals */
+		public List<GenomeLoc> getExons() { return exons; }
+		
+		/** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */ 
+	    public boolean overlapsP (GenomeLoc that) {
+	    	return transcript_interval.overlapsP(that);
+	    }
+		
+		/** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript. 
+		 * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
+		 * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript. 
+		 * @see overlapsExonP()
+		 */ 
+	    public boolean overlapsCodingP (GenomeLoc that) {
+	    	return transcript_coding_interval.overlapsP(that);
+	    }
+
+		/** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */ 
+	    public boolean overlapsExonP (GenomeLoc that) {
+	    	for ( GenomeLoc e : exons ) {
+	    		if ( e.overlapsP(that) ) return true;
+	    	}
+	    	return false;
+	    }
+
+	    /** Fills this object from a text line in RefSeq (UCSC) text dump file */
+		public void parseLine(String line) {
+			String[] fields = line.split("\t");
+			transcript_id = fields[1];
+			if ( fields[3].length()==1 && fields[3].charAt(0)=='+') strand = 1;
+			else if ( fields[3].length()==1 && fields[3].charAt(0)=='-') strand = -1;
+			else throw new StingException("Expected strand symbol (+/-), found: "+fields[3]);
+			
+			String contig_name = fields[2];
+			transcript_interval = new GenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
+			transcript_coding_interval = new GenomeLoc(contig_name, Integer.parseInt(fields[6])+1, Integer.parseInt(fields[7]));
+			gene_name = fields[12];
+			String[] exon_starts = fields[9].split(",");
+			String[] exon_stops = fields[10].split(",");
+			String[] eframes = fields[15].split(",");
+				
+			assert exon_starts.length == exon_stops.length : "Data format error: numbers of exon start and stop positions differ";
+			assert exon_starts.length == eframes.length : "Data format error: numbers of exons and exon frameshifts differ";
+			
+			exons = new ArrayList<GenomeLoc>(exon_starts.length);
+			exon_frames = new ArrayList<Integer>(eframes.length);
+			
+			for ( int i = 0 ; i < exon_starts.length  ; i++ ) {
+				exons.add(new GenomeLoc(contig_name, Integer.parseInt(exon_starts[i])+1, Integer.parseInt(exon_stops[i]) ) );
+				exon_frames.add(Integer.decode(eframes[i]));
+			}
+		}
+		
+}
+