PDE Nomenclature

NOMENCLATURE - BACKGROUND

SUMMARY OF CHANGES:

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Most recently updated on July 30, 1999


Table1 - CYCLIC NUCLEOTIDE PHOSPHODIESTERASE GENE FAMILIES

Short Name PDE Isozyme Gene Families Number of genes Number of reported Splice variants Evidence for additional splice variants.
PDE1 CaM-dependent PDEs 3 9+ yes
PDE2 cGMP-stimulated PDEs 1 2 yes
PDE3 cGMP-inhibited PDEs 2 2+ yes
PDE4 cAMP-specific PDES 4 15+ yes
PDE5 cGMP-specific PDEs 2 2 possible
PDE6 Photoreceptor PDEs 3 2 possible
PDE7 HCP1-PDE * 1 1 possible
* likely to be renamed when unique regulatory properties are identified

FIGURE 1: Explanation/Guidelines for Nomenclature in Table 2

Green----Species (first 2 letters)

Purple---PDE Gene Family (3 Capital Letters + 1 or 2 Arabic numerals)

Red------PDE Gene within family (Capital Letter)

Yellow---Splice variant (Arabic Numeral)

Blue-----Report ( Capital Letter)

example: HSPDE13A2A


The first two letters represent the species, for example HS for Homo sapiens. The next three letters plus one or two Arabic numerals designate the cyclic nucleotide phosphodiesterase gene family. The next letter represents the individual gene product within the family. The final Arabic numeral represents the splice variant and the final letter allows GenBank to assign a unique locus field designation based on when the entry was submitted and also to give different locus names to conflicting or incomplete sequences. It is hoped that most investigators will change their current GenBank LOCUS entries to this system and also will in the future use this nomenclature in the titles and abstracts of their manuscripts and in their GenBank submissions so that a commonly recognized order for nomenclature may be instituted. This system should allow for future expansion ( at least until the number of gene families or splice variants exceeds 99 or the number of genes within any one gene family exceeds 26). It was also the consensus of discussion that more descriptive names based on regulation and function continue to serve a useful role in the text of most manuscripts. For example, a paper on a PDE6 family member would be likely to include the terms "light activated or ROS or photoreceptor PDE" ; similarly one discussing the PDE2 family would be likely to include the terms "cGMP-stimulated PDE or cGS-PDE". Note, according to current Genbank rules, the GenBank LOCUS name must end in a letter, not a number.

A similar nomenclature system has been approved by the Human Genome Project Nomenclature Committee with the following differences. First, they omit the species since all are human sequences. Second, they use an asterisk followed by a second Arabic numeral to represent alleles rather than splice variants. The theoretical example shown above for a GenBank entry would be as follows in the Human Genome Entry. It is expected that the current names in the Human Genome data bank will be changed to reflect this new nomenclature.


Figure 2: HUMAN GENOME PROJECT NOMENCLATURE

Purple-----------PDE Gene family (3 Capital letters)

Purple + Red---Specific PDE Gene (PDE + Arabic numerals + letter)

Blue--------------Allele

example:PDE13A*2




TABLE II CYCLIC NUCLEOTIDE PDE ISOZYMES

Included in this table are most of the human, bovine and rodent cDNA references listed in GenBank or in recent literature references. Only those thought to be full length products or known to be catalytically active are listed. - GB = GenBank; - HuGP = Human Genome Project; - Acc Number = GenBank Accession Number;
---
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary*
--- PDE1 GENE FAMILY --- --- --- --- ---
--- BTPDE1A1A BOVBTPDE1A L34069> 59k CaM-PDE 8/91 comment
--- BTPDE1A2A BOVCNPA M90358 61k CaM-PDE 8/91 ---
--- BTPDE1B1A BOVCALPHOS M94867 63k CaM-PDE 9/92 ---
--- RNPDE1B1A RATCAMPDE M94537 63k CaM-PDE 9/92 ---
--- MMPDE1B1A MUSPDE1B1 L01695 63k CaM-PDE 12/92 ---
PDE1B HSU56976 HSPDE1B1A U56976 63k CaM-PDE 10/96 ---
PDE1C HSPDE1C1A HSPDE1C1A U40371 Hcam3b 1/96 comment
--- MMPDE1C1A MMPDE1C1A L76944 --- 10/96 ---
--- RNPDE1C2A RNPDE1C2A L41045 olf CaM-PDE 6/95 comment
PDE1C HSPDE1C3A HSPDE1C3A U43072 Hcam3a 1/96
--- MMPDE1C4A MMPDE1C4A L76947 --- 10/96 ---
--- MMPDE1C5A MMPDE1C5A L76946 --- 10/96 ---
--- PDE2 GENE FAMILY --- --- --- --- comment
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
--- BTPDE2A1A BOVCGMPCN M73512 cGS-PDE 10/91
--- RNPDE2A2A RNU21101 U21101 cGS-PDE 3/95
--- BTPDE2A3A BOVBTPDE2A L49503 cGS-PDE 2/96
PDE2A HSPDE2A3A HSU67733 U67733 cGS-PDE 5/97 ---
--- PDE3 GENE FAMILY --- --- --- --- comment
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
PDE3A HSPDE3A1A HUMGMPIPDI M91667 cGI-PDE 5/92 ---
--- RNPDE3B1A RNCAMPPHA Z22867 cGI-PDE 10/93 ---
--- PDE4 GENE FAMILY --- --- --- --- ---
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
--- RNPDE4A1A RATDUNCEA M26715,J04554 RD1 3/90 ---
--- RNPDE4A1B RATPHOSF L27062 RPDE8 12/93 ---
--- RNPDE4A2A RATDUNCEC M26717,J04554 RD2 3/90 comment
--- RNPDE4A3A RATDUNCEB M26716,J04554 RD3 3/90 comment
--- RNPDE4A?? RATPHOCNA M25348,M28411 ratPDE2 12/89 ---
PDE4A HSPDE4A1 hRD1 U97584 hRD1 01/98 ---
PDE4A HSPDE4A4A HUMPDEAA M37744 h-PDE1 1/91 comment
PDE4A HSPDE4A4B HUMPDEA L20965 PDE46 * 12/93 comment
PDE4A HSPDE4A4C HSU18087 U18087 hPDE4Ah6.1 2/95 comment
PDE4A HSPDE4A5? HUMPDEC L20967 DPDE2,TM3 7/93 ---
--- RNPDE4A5A RATPHOSA L27057 RPDE6 12/93 comment
--- RNPDE4A6 RAT35CA L36467 RAT35CA 3/95 comment
PDE4A HSPDE4A8A HSU18088 U18088 HSPDE4A7 8/95 comment
PDE4B HSPDE4B1A HUMPDEB L20966 TM72,DPDE4 7/93 ---
--- RNPDE4B1A RATDPD J04563 DPD 12/89 ---
PDE4B HSPDE4B2A HSPDE2A M97515 --- 6/93 ---
PDE4B HSPDE4B2B HUMPDEG L20971 PDE32 7/93 ---
PDE4B HSPDE4B2C HUMCAMPB L12686 --- 10/93 ---
--- RNPDE4B2A RATPHOCAMB M25350,M28413 ratPDE4 9/89 ---
--- RNPDE4B2B RATPHOSB L27058 RPDE18 12/93 ---
PDE4B HSPDE4B3A --- U85048 --- 01/98 ---
--- RNPDE4B3A --- U95748 RPDE74 01/98 ---
PDE4B HSPDE4B? ---- L12685 HPB102 10/93 comment
PDE4C HSPDE4C1A HUMPDED L20968 DPDE1,PDE21 7/93 ---
PDE4C HSPDE4C1B --- Z46632 --- 08/94
--- RNPDE4C1A RATPHOCN M25347,M28410 ratPDE1 9/89 ---
--- RNPDE4C1B RATPHOSE L27061 RPDE36 12/93 ---
PDE4C HSPDE4C2A --- U88712 --- 12/97 ---
PDE4C HSPDE4C3A --- U88713 --- 12/97 ---
PDE4C HSPDE4C4A --- U66346 4C791 12/97 ---
PDE4C HSPDE4C5A --- U66347 4C426 12/97 ---
PDE4C HSPDE4C6A --- U66348 4Cdelta54 12/97 comment
PDE4C HSPDE4C7A --- U66349 4Cdelta109 12/97 comment
PDE4D HSPDE4D1A --- U50157 --- 03/96 ---
PDE4D HSPDE4D1B --- U79571 DUN411 12/97 ---
--- RNPDE4D1A RATPHOCAMA U09455, M25349, M28412 ratPDE3.1 07/89 ---
--- RNPDE4D1B RATPHOSD L27060 RPDE13 12/93 ---
PDE4D HSPDE4D2A --- U50158 --- 03/96 ---
PDE4D HSPDE4D2B --- AF012074 PDE82 12/97 ---
--- RNPDE4D2A RATPDE32 U09456, M25349 ratPDE3.2 7/89 ---
PDE4D HSPDE4D3A HUMPDEF L20970 DPDE3,PDE43 12/93 ---
PDE4D HSPDE4D3B --- U50159 --- 03/96 ---
--- RNPDE4D3A RATPHOSC L27059 RPDE3 12/93 ---
--- RNPDE4D3B RATPDE33 U09457 ratPDE3.3 7/94 ---
PDE4D HSPDE4D4A HUMPDEE L20969 DPDE3,PDE39 12/93 ---
--- RNPDE4D4A --- AF031373 --- 12/97 ---
PDE4D HSPDE4D5A --- AF012073 PDE79 12/97 ---
PDE4D HSPDE4D?? --- U02882 h-PDEIVD 12/93 ---
--- PDE5 GENE FAMILY --- --- --- --- ---
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
--- BTPDE5A1 BOVPCGB8X L16545 cGB-PDE ## 10/93 ---
--- RNPDE5A2 D89093 D89093 --- 12/97 ---
--- PDE6 GENE FAMILY --- --- --- --- comment
HuGP Name
New GB LOCUS
 Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
PDE6A HSPDE6A1A HUMCGPRA M26061 ROS-PDEa 6/90 ---
--- BTPDE6A1A BOVCGMP01 M27541 ROS-PDEa 10/87 ---
--- BTPDE6A1B BOVCGPDAG M26043 ROS-PDEa 6/90 ---
--- MMPDE6A1A MMPA X60664 ROS-PDEa 8/91 ---
PDE6B HSPDE6B1A HSCGMPPM X66142 ROS-PDEb 8/93 ---
--- BTPDE6B1A BOVCGMP J05553 ROS-PDEb 6/90 ---
--- MMPDE6B1A MUSPDE X55968 ROS-PDEb 6/91 ---
--- MMPDE6B1B MMPB X60133 ROS-PDEb 8/91 ---
--- BTPDE6C1A BOVPDE M37838 Cone alpha' 6/90 ---
--- BTPDE6C1B BOVPDEAP M33140 Cone alpha' ^^ 6/90 ---
--- BTPDE6D1A BTPDE6D1A U65073 Rod delta 10/96 ---
PDE6G HSPDE6G1A HUMPDEGA M36476 Rod gamma 9/90 ---
--- BTPDE6G1A BTCGMPPR X04270 Rod gamma 6/87 ---
--- MMPDE6G1A MUSCGMPPD Y00746 Rod gamma 5/88 ---
--- BTPDE6H1A BOVPDEG J05578 Cone gamma 5/91 ---
--- PDE7 GENE FAMILY --- --- --- --- ---
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
PDE7A HSPDE7A1A HUMCAMPHOS L12052 HCP1 8/93 ---
--- HSPDE7A2A --- U68171 --- 11/96 ---
--- PDE8 GENE FAMILY --- --- --- --- ---
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
--- MMPDE8A --- AF067806 --- 7/98 ---
--- HSPDE8A --- AF056490 --- 6/98 "truncated"
--- HSPDE8B --- AF079529 --- 11/98 "truncated"
--- PDE9 GENE FAMILY --- --- --- --- ---
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
--- MMPDE9A1 --- AF031147 --- 6/98 ---
--- MMPDE9A2(?) --- AF068247 --- 6/98 ---
--- HSPDE9A2 --- AF048837 --- 6/98 ---
--- HSPDE9A1(?) --- AF067223 --- 7/98 ---
--- HSPDE9A2(?) --- AF067224 --- 7/98 ---
--- HSPDE9A3(?) --- AF067225 --- 7/98 ---
--- HSPDE9A4(?) --- AF067226 --- 7/98 ---
--- PDE10 GENE FAMILY --- --- --- --- ---
HuGP Name New GB LOCUS Old GB LOCUS ACC Number Alternate Name Pub Date Commentary
--- MMPDE10A --- AF110507 --- 5/99 ---
--- HSPDE10A --- AB020593 --- 6/99 ---
--- HSPDE10A1 --- AF127479 --- 5/99 ---
--- HSPDE10A2 --- AF127480 --- 5/99 "truncated"
^^ - Truncated version of PDE6C;

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