# RGD-PIPELINE: ftp-file-extracts
### As of Apr 1, 2011 RATMAP_IDs and RHDB_IDs are discontinued.
#COLUMN INFORMATION:
# (First 38 columns are in common between all species)
#
#1   GENE_RGD_ID	      the RGD_ID of the gene
#2   SYMBOL             official gene symbol
#3   NAME    	          gene name
#4   GENE_DESC          gene description (if available)
#5   CHROMOSOME_CELERA  chromosome for Celera assembly
#6   CHROMOSOME_3.1 chromosome for reference assembly build 3.1
#7   CHROMOSOME_3.4 chromosome for reference assembly build 3.4
#8   FISH_BAND          fish band information
#9   START_POS_CELERA   start position for Celera assembly
#10  STOP_POS_CELERA    stop position for Celera assembly
#11  STRAND_CELERA      strand information for Celera assembly
#12  START_POS_3.1   start position for reference assembly build 3.1
#13  STOP_POS_3.1    stop position for reference assembly build 3.1
#14  STRAND_3.1      strand information for reference assembly build 3.1
#15  START_POS_3.4   start position for reference assembly build 3.4
#16  STOP_POS_3.4    stop position for reference assembly build 3.4
#17  STRAND_3.4      strand information for reference assembly build 3.4
#18  CURATED_REF_RGD_ID     RGD_ID of paper(s) used to curate gene
#19  CURATED_REF_PUBMED_ID  PUBMED_ID of paper(s) used to curate gene
#20  UNCURATED_PUBMED_ID    PUBMED ids of papers associated with the gene at NCBI but not used for curation
#21  NCBI_GENE_ID           NCBI Gene ID
#22  UNIPROT_ID             UniProtKB id(s)
#23  GENE_REFSEQ_STATUS     gene RefSeq Status (from NCBI)
#24  GENBANK_NUCLEOTIDE     GenBank Nucleotide ID(s)
#25  TIGR_ID                TIGR ID(s)
#26  GENBANK_PROTEIN        GenBank Protein ID(s)
#27  UNIGENE_ID             UniGene ID(s)
#28  SSLP_RGD_ID            RGD_ID(s) of SSLPS associated with given gene
#29  SSLP_SYMBOL            SSLP symbol
#30  OLD_SYMBOL             old symbol alias(es)
#31  OLD_NAME               old name alias(es)
#32  QTL_RGD_ID             RGD_ID(s) of QTLs associated with given gene
#33  QTL_SYMBOL             QTL symbol
#34  NOMENCLATURE_STATUS    nomenclature status
#35  SPLICE_RGD_ID          RGD_IDs for gene splices
#36  SPLICE_SYMBOL          symbol for gene 
#37  GENE_TYPE              gene type
#38  ENSEMBL_ID             Ensembl Gene ID
#39  GENE_REFSEQ_STATUS_LEGACY legacy column -- use column 23 instead -- it will be discontinued in the future
#40  CHROMOSOME_5.0         chromosome for Rnor_5.0 reference assembly
#41  START_POS_5.0          start position for Rnor_5.0 reference assembly
#42  STOP_POS_5.0           stop position for Rnor_5.0 reference assembly
#43  STRAND_5.0             strand information for Rnor_5.0 reference assembly
#44  CHROMOSOME_6.0         chromosome for Rnor_6.0 reference assembly
#45  START_POS_6.0          start position for Rnor_6.0 reference assembly
#46  STOP_POS_6.0           stop position for Rnor_6.0 reference assembly
#47  STRAND_6.0             strand information for Rnor_6.0 reference assembly
#
GENE_RGD_ID	SYMBOL	NAME	GENE_DESC	CHROMOSOME_CELERA	CHROMOSOME_3.1	CHROMOSOME_3.4	FISH_BAND	START_POS_CELERA	STOP_POS_CELERA	STRAND_CELERA	START_POS_3.1	STOP_POS_3.1	STRAND_3.1	START_POS_3.4	STOP_POS_3.4	STRAND_3.4	CURATED_REF_RGD_ID	CURATED_REF_PUBMED_ID	UNCURATED_PUBMED_ID	NCBI_GENE_ID	UNIPROT_ID	GENE_REFSEQ_STATUS	GENBANK_NUCLEOTIDE	TIGR_ID	GENBANK_PROTEIN	UNIGENE_ID	SSLP_RGD_ID	SSLP_SYMBOL	OLD_SYMBOL	OLD_NAME	QTL_RGD_ID	QTL_SYMBOL	NOMENCLATURE_STATUS	SPLICE_RGD_ID	SPLICE_SYMBOL	GENE_TYPE	ENSEMBL_ID	GENE_REFSEQ_STATUS	CHROMOSOME_5.0	START_POS_5.0	STOP_POS_5.0	STRAND_5.0	CHROMOSOME_6.0	START_POS_6.0	STOP_POS_6.0	STRAND_6.0
1594427	2331ex4-5	class I gene fragment 2331		20		20	p12	150959	151483	-				2869836	2870560	-			15060004	415058		INFERRED	AABR07044364;AAHX01099425;BX883048;NG_004595				5029743;5046034	BI284484;RH131520					PROVISIONAL			pseudo		INFERRED	20	5330480	5331004	-	20	3232314	3232838	-
1594428	2310ex4-5	class I gene fragment 2310		20		20	p12	171896	172245	-				2890989	2891538	-			15060004	415055		INFERRED	AABR07044364;AAHX01099426;BX883048;NG_004594				5046076	RH131544					PROVISIONAL			pseudo		INFERRED	20	5351633	5351982	-	20	3253467	3253816	-
1500000	RAT    TY	It's a gene          silly		20		20	p12	140000	141000	-				2800000	2801000	-			14000000	141000		INFERRED	AABWHATEVER;NM1234;XM4321				5000000	RH123456					PROVISIONAL			pseudo		INFERRED	20	5000000	51000000	-	20	3000000	3100000	-
