MJB1%PHX.CAM.AC.UK@CUNYVM.CUNY.EDU (10/27/88)
Some of the gene names in the GenBank file GBHGM.IDX (release 57)
are not to be found in HGML at Yale.
In some cases it appears that the GenBank name is different from the
HGML name. In other cases there are mapped genes recorded in GenBank
which were not in HGML at 20 October 1988.
I have appended a list of the problem entries and would be grateful to
hear which of these are in HGML under a different name and which are
not in HGML. Thank you.
Martin Bishop.
*a (query) ADRBR *d HUMADRB1 PRI J03019 #
*a (query) BMD *d HUMDYSIN7 PRI M18024 #
*a (query) CALC1 *d HUMCAL PRI J00109 HUMCGRP PRI K03512
HUMCT PRI K03513 #
*a (query) HBE2 *d HUMHBB PRI J00179 #
*a (query) HBG *d HUMHBG3E PRI M11427 #
*a (query) HBZP1 *d HUMHBA3 PRI J00184 #
*a (query) HLA-DQ *d HUMMHDQAW PRI M16995 HUMMHDQBW PRI
M16996 #
*a (query) HLA-DQ1A *d HUMMHDQ PRI M11124 #
*a (query) HLA-DR *d HUMHLADA1 PRI M15372 HUMHLADA2 PRI
M15376 HUMHLADA3 PRI M15838 HUMHLADB1 PRI M15373 HUMHLADB2
PRI M15377 HUMHLADB3 PRI M15839 HUMHLADC1 PRI M15374
HUMHLADC2 PRI M15375 #
*a (query) HLA-DR1A *d HUMMHDRAM PRI K01171 HUMMHDRHA PRI
X00274 #
*a (query) HLA-DR1B *d HUMMHCDRB PRI M15397 HUMMHDR1B PRI
M11161 HUMMHDRBC PRI X02902 HUMMHDRBM PRI K02775 HUMMHDRBT
PRI K02776 HUMMHDRC PRI V00522 #
*a (query) HLA-DR3B *d HUMMHDRBB PRI X00699 HUMMHDRBD PRI
M13561 HUMMHDRBE PRI M13562 #
*a (query) HLA-DX1A *d HUMMHDXA1 PRI K01501 HUMMHDXA2 PRI
K01502 HUMMHDXA3 PRI K01503 HUMMHDXA4 PRI K01504 #
*a (query) IGD1 *d HUMIGCA2 PRI J00233 #
*a (query) SIS *d CATSISG5 MAM X03494 HUMSISA1 PRI K01918
HUMSISA2 PRI J00121 HUMSISA3 PRI K01398 HUMSISA4 PRI K01399
HUMSISA5 PRI K01400 HUMSISA6 PRI K01401 HUMSISPDG PRI M12783
#
*a (query) SPTA *d HUMSPA PRI M11049 #
*a (query) SRC1 *d HUMSRC101 PRI M16237 HUMSRC102 PRI M16243
HUMSRC103 PRI M16244 HUMSRC104 PRI M16245 HUMSRC105 PRI
K03212 HUMSRC106 PRI K03213 HUMSRC107 PRI K03214 HUMSRC108
PRI K03215 HUMSRC109 PRI K03216 HUMSRC110 PRI K03217
HUMSRC111 PRI K03218 #
*a (query) SRC2 *d HUMSRC2 PRI K03219 #
*a (query) T3D *d HUMATCT31 PRI M12726 HUMATCT32 PRI M12727
#jeh%life@LANL.GOV (Jamie Hayden) (11/16/88)
Dear Dr. Bishop,
Thank you for bringing these discrepancies between HGML and GenBank to our
attention. I apologize for the lateness of this response, but to give you
accurate answers I had to obtain the release of HGML which just came out.
Many of the discrepancies are old names which needed to be updated, a few are
typos, and others arose due to ambiguity of the gene. The problem entries are
included below followed by the action taken.
If you spot other inconsistencies or have problems in the future, please feel
free to contact me.
Jamie Hayden e-mail: jeh@life.LANL.GOV or
MS K710, T-10 genbank@LANL.GOV
LANL
Los Alamos, NM 87545 USA
tel: (505) 665-2587
*****************************************************************************
Date: Thu, 27 Oct 88 15:50:26 GMT
From: MJB1%PHX.CAM.AC.UK@CUNYVM.CUNY.EDU
To: genbankb@DL.AC.UK
Cc: generkt@YALEVM
Some of the gene names in the GenBank file GBHGM.IDX (release 57)
are not to be found in HGML at Yale.
In some cases it appears that the GenBank name is different from the
HGML name. In other cases there are mapped genes recorded in GenBank
which were not in HGML at 20 October 1988.
I have appended a list of the problem entries and would be grateful to
hear which of these are in HGML under a different name and which are
not in HGML. Thank you.
Martin Bishop.
*a (query) ADRBR *d HUMADRB1 PRI J03019 #
>ADRBR is the old name. Should be ADRB2R
*a (query) BMD *d HUMDYSIN7 PRI M18024 #
>should be DMD
*a (query) CALC1 *d HUMCAL PRI J00109 HUMCGRP PRI K03512
HUMCT PRI K03513 #
>CALC1 is the old name. Should be CALCA
*a (query) HBE2 *d HUMHBB PRI J00179 #
>should be HBE1
*a (query) HBG *d HUMHBG3E PRI M11427 #
>removed
*a (query) HBZP1 *d HUMHBA3 PRI J00184 #
>removed
*a (query) HLA-DQ *d HUMMHDQAW PRI M16995 HUMMHDQBW PRI
M16996 #
>hummhdqaw should be HLA-DQA
>hummhdqbw should be HLA-DQB
*a (query) HLA-DQ1A *d HUMMHDQ PRI M11124 #
>should be HLA-DQA
*a (query) HLA-DR *d HUMHLADA1 PRI M15372 HUMHLADA2 PRI
M15376 HUMHLADA3 PRI M15838 HUMHLADB1 PRI M15373 HUMHLADB2
PRI M15377 HUMHLADB3 PRI M15839 HUMHLADC1 PRI M15374
HUMHLADC2 PRI M15375 #
>removed
*a (query) HLA-DR1A *d HUMMHDRAM PRI K01171 HUMMHDRHA PRI
X00274 #
>HLA-DR1A is the old name. should be HLA-DRA1
*a (query) HLA-DR1B *d HUMMHCDRB PRI M15397 HUMMHDR1B PRI
M11161 HUMMHDRBC PRI X02902 HUMMHDRBM PRI K02775 HUMMHDRBT
PRI K02776 HUMMHDRC PRI V00522 #
>HLA-DR1B is the old name. should be HLA-DRB1
*a (query) HLA-DR3B *d HUMMHDRBB PRI X00699 HUMMHDRBD PRI
M13561 HUMMHDRBE PRI M13562 #
>HLA-DR3B is the old name. should be DRB3
*a (query) HLA-DX1A *d HUMMHDXA1 PRI K01501 HUMMHDXA2 PRI
K01502 HUMMHDXA3 PRI K01503 HUMMHDXA4 PRI K01504 #
>should be HLA-DXA
*a (query) IGD1 *d HUMIGCA2 PRI J00233 #
>IGD1 is the old name. Should be IGHDY1
*a (query) SIS *d CATSISG5 MAM X03494 HUMSISA1 PRI K01918
HUMSISA2 PRI J00121 HUMSISA3 PRI K01398 HUMSISA4 PRI K01399
HUMSISA5 PRI K01400 HUMSISA6 PRI K01401 HUMSISPDG PRI M12783
>SIS is the old name. Should be PDGFB
*a (query) SPTA *d HUMSPA PRI M11049 #
>should be SPTA1
*a (query) SRC1 *d HUMSRC101 PRI M16237 HUMSRC102 PRI M16243
HUMSRC103 PRI M16244 HUMSRC104 PRI M16245 HUMSRC105 PRI
K03212 HUMSRC106 PRI K03213 HUMSRC107 PRI K03214 HUMSRC108
PRI K03215 HUMSRC109 PRI K03216 HUMSRC110 PRI K03217
HUMSRC111 PRI K03218 #
>SRC1 is the old name. Should be SRC
*a (query) SRC2 *d HUMSRC2 PRI K03219 #
>SRC2 is the old name. Should be FGR
*a (query) T3D *d HUMATCT31 PRI M12726 HUMATCT32 PRI M12727
>T3D is the old name. Should be CD3D.
#
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