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