The Mouse Kinome: Comparison to Forrest et al.

A recent paper by Forrest et al also provides a catalog of mouse protein kinases as part of a 'phosphatome' (protein kinases + protein phosphatases) analysis . Their catalog lists 561 sequences as protein kinases. We attempted to obtain representative sequences for each of their kinase predictions and compared them to the kinome catalog to determine overlap and reasons for discrepancies.

There are 481 loci in common between the two gene sets. Genes found only in our work inlude most atypical kinases, several divergent kinases, a few of the MARK family expansions and a scattering of other kinases. Sequences found only in the Forrest et al paper include 13 sequences that we classify as psuedogenes, 32 sequences that duplicate previously-counted genes, and 36 additional sequences that do not appear to have clear kinase sequence homology. Some do have matches to the ProSite kinase domain motif (PS00107), which is known to suffer from some false positive predictions. Here are the details:

36 sequences found only in Forrest et al

We have not been able to find any connection between these sequences and known or predicted protein kinases.
CEPK556 CEPK45 CEPK551 CEPK553 CEPK521 CEPK555
CEPK489 CEPK462 CEPK500 CEPK490 CEPK527 CEPK547
CEPK381 CEPK499 CEPK472 CEPK529 CEPK561 CEPK560
CEPK559 CEPK503 CEPK530 CEPK525 CEPK550 CEPK524
CEPK141 CEPK523 CEPK168 CEPK82 CEPK458 CEPK549
CEPK101 CEPK269 CEPK533 CEPK498 CEPK534 CEPK528

Multiple phosphatome sequences matching a single kinome sequence

57 phosphatome sequences collapse into 25 kinome genes:
KinomePhosphatome
AMPKa2CEPK109, CEPK108, CEPK107, CEPK552
MarkmC1CEPK136, CEPK137, CEPK138
ULK1CEPK157, CEPK158, CEPK160
ULK4CEPK183, CEPK184
PKG1CEPK27, CEPK491
NRBP2CEPK492, CEPK493
PKG2CEPK28, CEPK522
EphA10CEPK379, CEPK382
ANPbCEPK455, CEPK456
CDK10CEPK466, CEPK468
CLK2CEPK440, CEPK442
CRK7CEPK479, CEPK481, CEPK482
DYRK1ACEPK445, CEPK449
EphB1CEPK378, CEPK386
FusedCEPK46, CEPK501, CEPK502
GAKCEPK483, CEPK484, CEPK485
HRICEPK509, CEPK510
IRAK3CEPK470, CEPK473
MAST2CEPK51, CEPK544
MASTLCEPK47, CEPK48
MUSKCEPK407, CEPK408
SgK495CEPK148, CEPK545
skMLCKCEPK174, CEPK71
smMLCKCEPK177, CEPK299
TRKACEPK405, CEPK406

Phosphatome sequences which match kinome pseudogenes

11 phosphatome sequences match kinase pseudogenes, and a futher two match 'rs' sequences that are likely pseudogenes and classified as such in our analysis.
PhosphatomeKinome
CEPK123 MarkmB2ps
CEPK221 CDK8ps
CEPK18 PKCeps
CEPK44 ROCK1ps
CEPK134 MarkmDps1
CEPK460 CDK4ps1
CEPK461 CDK6ps2
CEPK132 MarkmDps4
CEPK463 CDK4ps4
CEPK467 CDK10ps
CEPK465 CDK3ps
CEPK121 MarkmB1-rs
CEPK37 NDR2-rs

59 kinases found in our work but not by Forrest

ClassGenes
Atypical: A6 familyA6, A6r
Atypical: ABC1 familyADCK2, ADCK4, ADCK5
Atypical: Alpha Kinase familyAlphaK1, AlphaK2, AlphaK3, ChaK1, ChaK2, eEF2K
Atypical: BRD familyBRD2, BRD3, BRD4, BRDT
Atypical: PDHK familyPDHK1, PDHK2, PDHK3, PDHK4, BCKDK
Atypical: RIOK familyRIOK2, RIOK3
Atypical: TIF1 familyTIF1a, TIF1b, TIF1g
Atypical: PIKK familyATM, ATR, DNAPK, FRAP, SMG1, TRRAP
Atypical: VariousBCR, FASTK, G11, H11, TAF1
CAMK:CAMKL:MARK subfamilyMarkmA4, MarkmA6, MarkmA7, MarkmA10, MarkmA12, MarkmB2, MarkmC2, MarkmD1, MarkmD4, MarkmE1, MarkmE3
ePK: VariousAAK1, AMPKa1, AurC, Dyrk2, EphA6, Myo3B, SgK071, SgK085, SgK110, SgK424, SgK493

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