Rat Cytochrome P450s

Note on Jan. 24, 2007 I started this page. Completed April 27, 2007

The rat genome has 88 P450 genes and 69 P450 pseudogenes.

This table has over 850 links to sequence and map data

I include seven gene cluster maps that show human, mouse and rat compared (red links in the first column).

These map links are also included in the human master table. These maps are further described in:

Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes

Pharmacogenetics 14, 1-18 2004

The maps and the nucleotide numbering in the protein sequence links were based

on an earlier version of the rat genome assembly, so the numbers are a little

different from the new UCSC browser nucleotide numbering.

Current UCSC links are based on the Nov. 2004 assembly.

My first links to UCSC were unstable. I have now replaced those links with a

stable format: http://genome.ucsc.edu/cgi-bin/hgTracks?org=rat&db=rn4&position=chr8%3A61350064-61538088

These links should be permanent.

The Entrez Gene links have extensive data and links for intact sequences and some pseudogenes.

For a complete set of rat P450 sequences including pseudogenes go to the FASTA file

All rat P450 genes and all P450 pseudogenes will be included in this table.

CYP names in column 1 are linked to their protein sequences, including the pseudogenes.

X at the end of a CYP name means that name has been discontinued and replaced by a new name

Pseudogenes are named using suffixes to specify the four types of pseudogenes defined as:

P is a full length or near full length pseudogene, it may be near or far from other P450s.

-ps is equivalent to P, but it is required nomenclature for mouse and rat full length pseudogenes.

-de stands for detritus exons (found near other full length genes).

-se stands for solo exons, one or a few exons found distant from a P450 gene.

-ie stands for internal exons, duplicate exons found inside some P450 genes.

Cyp	Genbank	RefSeq mRNA	Genomic Assemblies	RefSeq Protein	UCSC genome browser	Unigene	EntrezGene	comments
1a1	see related sequences under the Entrez Gene link	NM_012540	see reference assembly under the Entrez Gene link	NP_036672	Cyp1a1 and 1a2	Rn.10352 (4 ESTs)	Cyp1a1	8q24, Chr8: 61464759- 61467268 (+) strand
1a2	see related sequences under the Entrez Gene link	NM_012541	see reference assembly under the Entrez Gene link	NP_036673	Cyp1a1 and 1a2	Rn.5563 (9 ESTs)	Cyp1a2	8q24, Chr8: 61439330- 61445517 (-) strand
1b1	see related sequences under the Entrez Gene link	NM_012940	see reference assembly under the Entrez Gene link	NP_037072	Cyp1b1	Rn.10125 (15 ESTs)	Cyp1b1	6q11, Chr6: 2548542- 2553015 (-) strand
2a1 2ABFGST gene cluster map	see related sequences under the Entrez Gene link	NM_012692	see reference assembly under the Entrez Gene link	NP_036824	Cyp2abfgst cluster	Rn.32107 (17 ESTs)	Cyp2a1	1q21, Chr1: 82006847- 82020093 (+) strand, Cyp2a22 mouse ortholog
2a1-de2b	M33312.1	no entry	no entry	no entry	Cyp2a1-de2b	no entry	no entry	1q21, Chr1: 82006542- 82006607 (-) strand, upstream of 2a1 on opp strand, frag e in 2a cluster map
2a2	see related sequences under the Entrez Gene link	NM_012693	see reference assembly under the Entrez Gene link	NP_036825	Cyp2a1 and 2a2	Rn.9867 (16 ESTs)	Cyp2a2	1q21, Chr1: 82039238- 82063522 (+) strand, Cyp2a12 mouse ortholog
2a2-de2b	M33312.1	no entry	no entry	no entry	Cyp2a2-de2b	no entry	no entry	1q21, Chr1: 82037313- 82037417 (-) strand, upstream of 2a2 on opp strand, frag f in 2a cluster map
2a3	see related sequences under the Entrez Gene link	NM_012542	see reference assembly under the Entrez Gene link	NP_036674	Cyp2a1, 2a2, 2a3	Rn.2063 (3 ESTs)	Cyp2a3	1q21, Chr1: 81944896- 81952812 (+) strand, Cyp2a5 mouse ortholog
2a3-de1b	multiple	no entry	no entry	no entry	Cyp2a3-de1b	no entry	no entry	1q21, Chr1: 81974029- 81974133 (+) strand, downstream of 2a3 on same strand, frag d in 2a cluster map
2b1 2ABFGST gene cluster map	multiple	XM_001070869	AAHX01004337	multiple	Cyp2b1 center seq. Gene to the right is Cyp2b2	no entry, improperly merged with Cyp2b2	Cyp2b1	1q21, chr1:81266845- 81290085, ortholog of mouse Cyp2b10
2b2	J00720-J00728	no entry	AAHX01004340	multiple	Cyp2b2 right side seq. Gene to the left is Cyp2b1	Rn.91353 (33 ESTs), improperly merged with Cyp2b1	Cyp2b2	1q21, chr1:81345425- 81359030, ortholog of mouse Cyp2b13
2b3	see related sequences under the Entrez Gene link	NM_173294	see reference assembly under the Entrez Gene link	NP_775416	Cyp2b3 exons 1-8, exon 9 is misplaced	Rn.4845 (57 ESTs)	Cyp2b3	1q21, chr1: 81408456- 81459262, exon 9 81185069- 81185251, genome assembly error, exon 9 is in the wrong place, does not match ESTs that support Cyp2b3, ortholog of mouse Cyp2b9
2b3-se1[9]	no entry	no entry	no entry	no entry	Cyp2b3- se1[9] exon 9 pseudogene	no entry	no entry	1q21, exon 9 pseudogene, 81185069- 81185251, genome assembly error?, 100% match to Cyp2b3 mRNA upstream of Cyp2b1, fragment a in Cyp2abfgst cluster map
2b3-se2[1]	no entry	no entry	no entry	no entry	Cyp2b3- se2[1] exon 1 pseudogene	no entry	no entry	1q21, exon 1 pseudogene, 81230276- 81230446, 100% match to Cyp2b3 mRNA upstream of Cyp2b1 on opposite strand, fragment b in Cyp2abfgst cluster map
2b12	X63545	NM_017156	NC_005100.2 from 81780088 to 81791770	NP_058852	center gene, Cyp2b32-ps left side seq., Cyp2b31 right side sequence. Incorrectly labled Cyp2b15 in UCSC browser	Rn.144570 (0 ESTs), incorrectly named Cyp2b15	Cyp2b12 (X63545 seq), warning misnamed Cyp2b15 and includes Cyp2b1 accessions, needs major revision	1q21, chr1:81780127- 81791000, Cyp22b12, 2b15 and 2b31 are possible paralogs of mouse Cyp2b19, see map
2b12-de9b	no entry	no entry	AAHX01004353 from 5896 to 6075 (+) strand	no entry	small left side seq., Cyp2b12 on the right side is mistakenly labeled Cyp2b15.	no entry	no entry	1q21, chr1:81750901- 81751080, upstream of Cyp2b12 on opposite strand, frag. c in Cyp2abfgst cluster map
2b14-ps	U33540	no entry	AAHX01004350 from 49244 to 70481	no entry	Cyp2b14-ps left side seq., Cyp2b21 right side seq.	no entry	no entry	1q21, Chr1:81628189- 81650662 (+) strand
2b15	D17343 to D17349	no entry	AABR03002513 from 29026 to 29202 (+) strand, exon 1 AAHX01004359 from 4054 to 12264 (-) strand, exons 4-9	no entry	right side seq. (exons 1,5-9), left side seq. = Cyp2b31	no entry, the Cyp2b15 entry is actually Cyp2b12	no entry, the Cyp2b15 entry is a mixture of Cyp2b12 and Cyp2b1	1q21, chr1:81866957- 81879265 (+) strand, exons 2-4 in a seq gap
2b16-ps	U33541 to U33545 U33546	no entry	AAHX01004347 from 5656 to 31499 (-) strand	no entry	Cyp2b16-ps lies between 2b3 and 2b14p	no entry	no entry	1q21, Chr1: 81555838- 81581670 (+) strand
2b21	see related sequences under the Entrez Gene link	NM_198733	see reference assembly under the Entrez Gene link	NP_942028	Cyp2b21 lies between 2b14p and 2b32-ps	Rn.38261 (2 ESTs) incorrectly named Cyp2b13	CYP2b21 incorrectly named Cyp2b13 (a mouse gene)	1q21, chr1: 81658529- 81687115, (-) strand, ortholog of mouse Cyp2b23
2b31	XM_577774	XM_577774	AABR03002513 from 1999 to 14226 (+) strand	XP_577774	Cyp2b31 lies between 2b12 and 2b15	no entry	no entry	1q21, chr1: 81839930- 81852357, (+) strand, Cyp2b31, 2b12 and 2b15 are possible paralogs of mouse Cyp2b19, see map
2b32-ps	XM_001077535 nucl. 31-636 matches exons 2,4,5 and 6, the rest is Cyp2b12	no entry	AAHX01004351 from 1039 to 6308 (-) strand	no entry	Cyp2b32-ps lies between 2b21 and 2b12	no entry	no entry	1q21, chr1: 81728417- 81733686, (+) strand
2c6v1 2C gene cluster map	M13711 and other entries in Entrez Gene	XM_001066767.1	NW_047565.2 from 12042110 to 12081061 (+) strand. See also assemblies in Entrez gene	XP_001066767.1	upstream of Cyp2c7	Rn.91122 (397 ESTs), Cyp2c6 Rn.160031 (4 ESTs), Cyp2c6	Cyp2c6	1q53, NW_047565.2 from 12042110 to 12081061 (+) strand, upstream of 2c7
2c6v1- de1b2b3b4b5b	no entry	no entry	NW_047565.2 from 12022325 to 12026993 (+) strand.	no entry	upstream of Cyp2c6v1	no entry	no entry	1q53, NW_047565.2 from 12022325 to 12026993 (+) strand, upstream of 2c6v1, fragment o, 96% identical to fragment c
2c6-se1 [1:2:3:2:3]	no entry	no entry	NW_047565.2 from 12131467 to 12139285 (+) strand	no entry	downstream of Cyp2c6	no entry	no entry	1q53, NW_047565.2 from 12131467 to 12139285 (+) strand, downstream of 2c6, fragments m+n in map.
2c7	M18335 also see other entries in Entrez Gene	NM_017158.1	NW_047565.2 from 11885812 to 11915970 (+) strand. N-term in a seq gap. See also assemblies in Entrez gene	NP_058854.1	upstream of Cyp2c6	Rn.1247 (25 ESTs), Cyp2c7	Cyp2c7	1q53, NW_047565.2 from 11885812 to 11915970 (+) strand, upstream of 2c6
2c7-de7b	no entry	no entry	NW_047565.2 from 11879492 to 11879677 (+) strand	no entry	downstream of Cyp2c7	no entry	no entry	1q53, NW_047565.2 from 11879492 to 11879677 (+) strand, fragment r on map downstream of Cyp2c7, 100% to frag a CYP2C81-de7b
2c7-se1 [2:3:6:7:9]	no entry	no entry	NW_047565.2 from 12150684 to 12210973 (+) strand	no entry	upstream of Cyp2c82-ps	no entry	no entry	1q53, NW_047565.2 from 12150684 to 12210973 (+) strand, between 2c6 and 2c82-ps, fragments j+k in map. Nearly identical to 2c7
2c7-se3[8]	no entry	no entry	NW_047565.2 from 11836177 to 11836314 (-) strand	no entry	downstream of Cyp2c7	no entry	no entry	1q53, NW_047565.2 from 11836177 to 11836314 (-) strand, fragment t on map downstream of Cyp2c7
2c7-se4[8:9]	no entry	no entry	NW_047565.2 from 11809387 to 11812694 (-) strand	no entry	downstream of Cyp2c7	no entry	no entry	1q53, NW_047565.2 from 11809387 to 11812694 (-) strand, fragment u on map downstream of Cyp2c7, 87% to Cyp2c81-de8c frag 2
2c11	multiple	NM_019184	AAHX01000338 from 94107 to 107640 (+) strand, aa 1-276 AAHX01000339 from 4340 to 20589 (-) strand, aa 274-500	NP_062057	Cyp2c11 at the centromeric edge of the 2c cluster, adjacent to hells	Rn.10870 (258 ESTs), called Cyp2c in Unigene	Cyp2c11	1q53, Chr1: 243281340- 243320612, male specific, Cyp2c52-ps mouse ortholog
2c12	see related sequences under the Entrez Gene link	NM_031572	NW_001084775 from 133145 to 189992 (-) strand	NP_113760	Cyp2c12, downstream of Cyp2c13, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	Rn.2586 (697 ESTs)	Cyp2c12, female specific, mistakenly called Cyp2c40, paralog of the mouse Cyp2c40, 2c67, 2c68 and 2c69 genes	1q53, NW_001084775 from 133145 to 189992 (-) strand
2c12-de8b	no entry	no entry	NW_001084775 from 127088 to 127213 (-) strand	no entry	downstream of Cyp2c12, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	no entry	no entry	1q53, NW_001084775 from 127088 to 127213 (-) strand, 6 kb downstream of 2c12, 1 amino acid diff. to Cyp2c81-de8c
2c13	see related sequences under the Entrez Gene link	NM_138514	NW_001084775 from 219120 to 300164 (-) strand	NP_612523	Cyp2c12, downstream of Cyp2c13, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	Rn.82715 (132 ESTs)	Cyp2c13, paralog of the mouse Cyp2c40, 2c67, 2c68 and 2c69 genes	1q53, NW_001084775 from 219120 to 300164 (-) strand
2c13-de1b2b	no entry	no entry	NW_001084775 from 339611 to 353773 (-) strand	no entry	downstream of Cyp2c12, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	no entry	no entry	1q53, NW_001084775 from 339611 to 353773 (-) strand, fragments 6,7 upstream of Cyp2c13
2c13-de4c5c	no entry	no entry	NW_001084775 from 202080 to 203586 (+) strand	no entry	downstream of Cyp2c12, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	no entry	no entry	1q53, NW_001084775 from 202080 to 203586 (+) strand, new fragment between Cyp2c12 and Cyp2c13
2c13-se1[6]	no entry	no entry	NW_047565.2 from 12251668 to 12251809 (+) strand	no entry	upstream of Cyp2c82-ps	no entry	no entry	1q53, NW_047565.2 from 12251668 to 12251809 (+) strand, upstream of Cyp2c82-ps, fragment h in map. Identical to a fragment near fragment v in map
2c13-se2[6:7]	no entry	no entry	NW_047565.2 from 11846494 to 11852957 (-) strand	no entry	downstream of Cyp2c7	no entry	no entry	1q53, NW_047565.2 from 11846494 to 11852957 (-) strand, fragment s on map downstream of Cyp2c7, identical to frag h
2c13-se3 [1:2:3:2:3:]	no entry	no entry	NW_047565.2 from 12299636 to 12301994 (-) strand	no entry	upstream of Cyp2c82-ps	no entry	no entry	1q53, NW_047565.2 from 12299636 to 12301994 (-) strand, upstream of Cyp2c82-ps, fragment f in map. Identical to fragment v in map
2c13-se4 [1:2:3]	no entry	no entry	NW_047565.2 from 11765188 to 11766652 (+) strand	no entry	between frags u and x	no entry	no entry	1q53, NW_047565.2 from 11765188 to 11766652 (+) strand, downstream of Cyp2c7, fragment v in map. Identical to fragment f
2c22	see related sequences under the Entrez Gene link	NM_138512	see reference assembly under the Entrez Gene link	NP_612521	Cyp2c22, on the telomeric edge of the 2c cluster, next to Pdlim1	Rn.88025 (223 ESTs)	Cyp2c22, mistakenly called Cyp2c70 for the mouse ortholog	1q53, chr1: 245298599- 245329426 Cyp2c70 mouse ortholog
2c22-se1[8]	no entry	no entry	NW_047565.2 from 12288092 to 12288164 (-) strand	no entry	upstream of Cyp2c82-ps	no entry	no entry	1q53, NW_047565.2 from 12288092 to 12288164 (-) strand, upstream of Cyp2c82-ps, fragment g in map. Identical to two fragments near fragment v in map
Cyp2c22- se2[1:2]	no entry	no entry	NW_001084775 from 376374 to 389507 (+) strand	no entry	downstream of Cyp2c12, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	no entry	no entry	1q53, NW_001084775 from 376374 to 389507 (-) strand, 48kb downstream of Cyp2c22, fragments 8,9 on map
2c22-se3[8]	no entry	no entry	NW_047565.2 from 11774859 to 11774931 (+) strand	no entry	between frags u and v	no entry	no entry	1q53, NW_047565.2 from 11774859 to 11774931 (+) strand, downstream of Cyp2c7, fragment 10 in map. Identical to fragment g
2c22-se4[8]	no entry	no entry	NW_047565.2 from 11776742 to 11776814 (+) strand	no entry	between frags u and v	no entry	no entry	1q53, NW_047565.2 from 11776742 to 11776814 (+) strand, downstream of Cyp2c7, fragment 11 in map. Identical to fragment g
2c23	see related sequences under the Entrez Gene link	NM_031839.2	NW_047566.2 from 2165733 to 2189928 (+) strand NW_001084775 from 4291818 to 4316013 (-) strand	NP_114027	Cyp2c23, 4.1 Mb from the 2c cluster, flanked by Erlin1 and Cpn1	Rn.2184 (286 ESTs)	Cyp2c23	1q54, chr1: 249204073- 249228265 Cyp2c44 mouse ortholog
2c24	M86678	XM_574665.2	NW_001084774.1 from 50448200 to 50492967 (+) strand, first exon on EST CK481568.1	XP_574665.2	downstream of Cyp2c211, assembly in error here	Rn.198563 (1 EST)	RGD1563697 predicted, partial seq of Cyp2c24	1q53, chr1: 243422110- 243425514 Cyp2c55 mouse ortholog, orientation in conflict, probably in gene order 2C11(+), 2C24(+), 2C80(+), 2C79(+), with 2C79 and 2C80 in the wrong location on the map
2c77-ps	no entry	no entry	NW_047565.2 from 12444376 to 12482016 (+) strand	no entry	Cyp2c77-ps, downstream from 2c82-ps, the gene has three frameshifts	no entry	LOC686022, includes Cyp2c77- de1b2b3b4b5b	1q53, chr1: 244261291- 244298928, 13 aa diffs to Cyp2c6_v1, paralog to mouse 2c29, 2c38, 2c39
2c77- de1b2b3b4b5b	no entry	no entry	NW_047565.2 from 12424424 to 12429575 (+) strand	no entry	Cyp2c77- de1b2b3b4b5b, downstream from 2c82-ps	no entry	LOC686022, includes Cyp2c77-ps	1q53, chr1: 244241339- 244246490, 9 aa diffs to CYP2C6v1_v1- de1b2b3b4b5b, 2c77-ps and its pseudogene result from a block duplication of 2c6_v1 and its pseudogene
2c79	XM_219933.3 complete	XM_001080345 partial, XM_219933.3 complete	NW_001084774.1 from 50635105 to 50699203 (+) strand, partial seq exons 4-7	XP_219933.2 complete, XP_001080345 partial	downstream of Cyp2c211, assembly in error here	Rn.154478 (1 EST)	Cyp2c65 predicted, paralog of mouse Cyp2c65 and 2c66	1q53, chr1: NW_001084774 50635105 to 50699203 (+) probably in gene order 2C11(+), 2C24(+), 2C80(+), 2C79(+), with 2C79 and 2C80 in the wrong location on the map
2c79-de9b	no entry	no entry	NW_047565.2 from 12577788 to 12577898 (-) strand	no entry	downstream of Cyp2c79, assembly may be in error here	no entry	no entry	1q53, NW_047565.2 from 12577788 to 12577898 (-) strand, fragment b on map downstream of Cyp2c79
Cyp2c79-se1[9]	no entry	no entry	NW_047565.2 from 11971674 to 11971853 (+) strand.	no entry	between Cyp2c6v1 and 2c7	no entry	no entry	1q53, NW_047565.2 from 11971674 to 11971853 (+) strand, upstream of 2c6v1, fragment p, 100% identical to Cyp2c79 exon 9
2c80	XM_001080338 complete	XM_001080338 complete, XM_217906.4 partial	NW_001084774.1 from 50565229 to 50609865 (+) strand	XP_001080338 complete, XP_217906.4 partial	downstream of Cyp2c211, assembly in error here	Rn.154468 (1 EST)	Cyp2c55 predicted, ortholog of mouse Cyp2c55, 91% to Cyp2c24	1q53, chr1: NW_001084774 50565229 to 50609865 (+) probably in gene order 2C11(+), 2C24(+), 2C80(+), 2C79(+), with 2C79 and 2C80 in the wrong location on the map
2c81	Gnomon model: hmm62430, N-term incorrect	XM_001058491.1, not accurate	NW_047565.2 from 12758605 to 12805314 (+) strand	XP_001058491.1, not accurate	in a region of uncertainty	no entry	no entry	1q53, chr1: NW_047565.2 from 12758605 to 12805314 (+) strand, missing exon 1
2c81-de7b	no entry	no entry	NW_047565.2 from 12810967 to 12811155 (-) strand	no entry	in a region of uncertainty	no entry	no entry	1q53, NW_047565.2 from 12810967 to 12811155 (-) strand, fragment a on map downstream of Cyp2c81
2c81-de8b	no entry	no entry	NW_047565.2 from 12823758 to 12823898 (+) strand	no entry	in a region of uncertainty	no entry	no entry	1q53, NW_047565.2 from 12823758 to 12823898 (+) strand, fragment 1 on map downstream of Cyp2c81
2c81-de8c	no entry	no entry	NW_047565.2 from 12850765 to 12850905 (+) strand	no entry	in a region of uncertainty	no entry	no entry	1q53, NW_047565.2 from 12850765 to 12850905 (+) strand, fragment 2 on map downstream of Cyp2c81
2c81-de1d	no entry	no entry	NW_001084775 from 6139 to 6294 (+) strand	no entry	downstream of Cyp2c12, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	no entry	no entry	1q53, NW_001084775 from 6139 to 6294 (+) strand, downstream of 2c12, fragment 3 on map
2c81-de6e7e	no entry	no entry	NW_001084775 from 23979 to 24128 (+) strand	no entry	downstream of Cyp2c12, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	no entry	no entry	1q53, NW_001084775 from 23979 to 24128 (+) strand, downstream of 2c12, fragment 4 on map
2c81- de1f2f3f	no entry	no entry	NW_001084775 from 35664 to 49635 (-) strand	no entry	downstream of Cyp2c12, this fragment is unmapped but Cyp2c12 and Cyp2c13 are mapped downstream of 2c22 on NW_001084775	no entry	no entry