News

24 August 2019|New LRG XML schema 1.10:

The LRG XML schema has been updated with the following changes:

“MANE Select” flag

The most significant change is the inclusion of the “MANE” attributes in order to display transcripts selected as part of our new initiative, the MANE (Matched Annotation from the NCBI and EMBL-EBI) Project.

This joint initiative between Ensembl/GENCODE Project and NCBI’s RefSeq project aims to release a genome-wide transcript set that contains one well-supported transcript per protein-coding locus (MANE Select). All transcripts in the MANE set perfectly align to GRCh38 and represent 100% identity (5’UTR, coding sequence, 3’UTR) between the RefSeq (NM) and corresponding Ensembl (ENST) transcript. Currently, a MANE Select transcript has been defined for ~67% of protein-coding loci. The MANE project also aims to release an expanded set (MANE Plus) to include additional transcripts per locus that are well-supported or of particular user interest. For more information on MANE see Ensembl’s MANE blog and the NCBI’s MANE blog.

The MANE-select and MANE-plus values have been added to the source attribute of the db_xref XML tag. This allows us to display the “MANE Select” flag in the Fixed and Updatable sections of records. Our aim is to clarify the difference, if any, with LRG transcripts. Also, MANE transcripts are displayed as a Genoverse track in the “Mapping section” of records.


New tag “superceded_by”

In the future, some LRGs could be deprecated and superseded by new ones. These new records will be for the same gene as their predecessor, but will have a different identifier and different reference sequences. A record can be deprecated if knowledge about the LRG transcript(s) in the Fixed section has changed significantly (i.e. changes to the position of the start ATG or changes to protein coding exons). Given that we cannot remove or replace transcripts in the Fixed Section, the only way to provide accurate information about an LRG transcript that has changed is to create a new record that includes the updated version of the transcript.
If your favourite LRG has been superseded and you would like more information, please contact us at contact@lrg-sequence.org.


New “type” attributes for the “mapping” tags

The “type” attributes fix_patch and novel_patch have been added to the “mapping” tag, for more clarity.


The full history of the LRG XML schema changes can be found here.


04 June 2019|10new LRGs made public:

HGNC symbolLRG ID
ACAT1LRG_1400
AKT2LRG_1391
AKT3LRG_1396
DDR2LRG_1390
ETNK1LRG_1399
JAK1LRG_1398
KRASLRG_344
PIK3R2LRG_1392
RYR2LRG_402
SMOLRG_1393
See more details here

07 May 2019|14new LRGs made public:

HGNC symbolLRG ID
BARD1LRG_297
CBFBLRG_1364
DDX41LRG_1386
DEKLRG_1375
GREM1LRG_1365
NTHL1LRG_1366
NUP214LRG_1383
HGNC symbolLRG ID
PAX5LRG_1384
PTPRZ1LRG_1387
RIT1LRG_1372
SCN8ALRG_1389
STAT6LRG_1369
TACC3LRG_1367
TMPRSS2LRG_1368
See more details here

03 April 2019|2new LRGs made public:

HGNC symbolLRG ID
CLPBLRG_1338
RORCLRG_1322
See more details here

26 March 2019|30new LRGs made public:

HGNC symbolLRG ID
CARD14LRG_1330
COPALRG_1336
IL17RCLRG_1311
IRF7LRG_1313
ISG15LRG_1231
ITGAMLRG_1333
LRBALRG_1324
NFAT5LRG_1332
NFKB1LRG_1316
NFKB2LRG_1347
HGNC symbolLRG ID
NLRC4LRG_1317
PARNLRG_1286
PGM3LRG_1312
PRKCDLRG_1327
PSMB8LRG_1328
RNF31LRG_1315
SART3LRG_1285
SEMA3ELRG_1287
SH3BP2LRG_1334
SLC29A3LRG_1318
HGNC symbolLRG ID
STAT2LRG_1329
TBK1LRG_1306
TCF3LRG_1325
TMEM173LRG_1308
TNFRSF4LRG_1319
TNFSF12LRG_1320
TPP2LRG_1341
TRAF3IP2LRG_1337
TRNT1LRG_1314
TTC7ALRG_1323
See more details here

10 October 2018|5new LRGs made public:

HGNC symbolLRG ID
FCGR3BLRG_1238
IKBKBLRG_1241
IL10LRG_1230
IL21LRG_1263
IL22LRG_1248
See more details here

24 August 2018|8new LRGs made public:

HGNC symbolLRG ID
CPOXLRG_1077
CYP1A1LRG_1262
CYP1A2LRG_1274
CYP2B6LRG_1267
CYP2C9LRG_1195
CYP2D6LRG_303
HMBSLRG_1076
URODLRG_1079
See more details here

15 August 2018|17new LRGs made public:

HGNC symbolLRG ID
ACDLRG_1237
AGKLRG_1251
ALDOBLRG_1244
ALG6LRG_1260
ALOX12BLRG_1264
ALX3LRG_1265
ALX4LRG_1256
AP5Z1LRG_1247
BBS10LRG_1255
HGNC symbolLRG ID
CHRNELRG_1254
COL17A1LRG_1249
COL9A3LRG_1253
COX6B1LRG_1246
COX7BLRG_1250
DOCK2LRG_1227
DSPPLRG_1242
MTHFD1LRG_1243
See more details here

04 July 2018|16new LRGs made public:

HGNC symbolLRG ID
ACP5LRG_1218
ADA2LRG_1217
B2MLRG_1215
CFHR4LRG_1224
CTLA4LRG_1220
CTPS1LRG_1229
DCLRE1BLRG_1219
EPG5LRG_1234
HGNC symbolLRG ID
IFIH1LRG_1235
IL17ALRG_1223
INO80LRG_1233
JAGN1LRG_1228
MALT1LRG_1221
MAP3K14LRG_1222
MCM4LRG_1239
MOGSLRG_1226
See more details here

23 May 2018|17new LRGs made public:

HGNC symbolLRG ID
ABCB7LRG_1162
ADARLRG_1212
BCL10LRG_1210
CFHR2LRG_1216
CTC1LRG_1124
FBXW7LRG_1141
GPILRG_1178
GSSLRG_1168
KIF23LRG_1173
HGNC symbolLRG ID
NOTCH1LRG_1122
PRKG1LRG_1135
RPS10LRG_1138
RPS26LRG_1146
RPS27LRG_1158
SLC2A1LRG_1132
SRP72LRG_1151
VPS13DLRG_1213
See more details here

16 May 2018|45new LRGs made public:

HGNC symbolLRG ID
ABCB11LRG_1199
ABCC2LRG_1208
ADAM17LRG_1203
ALAS2LRG_1163
AP3D1LRG_1207
ARHGAP26LRG_1127
ARPC1BLRG_1188
ATP1A3LRG_1186
ATP8B1LRG_1205
ATRXLRG_1153
C8GLRG_1211
CBLBLRG_1179
HGNC symbolLRG ID
CBLCLRG_1161
CCBE1LRG_1209
CDAN1LRG_1164
DNAJC21LRG_1214
EPB42LRG_1171
ENO1LRG_1165
FOXF2LRG_1190
GCLCLRG_1166
JAG1LRG_1191
KDSRLRG_1196
KNG1LRG_598
HGNC symbolLRG ID
PIEZO1LRG_1137
PKLRLRG_1136
RPL5LRG_1155
RPL11LRG_1140
RPL15LRG_1152
RPL19LRG_1120
RPL26LRG_1125
RPL27LRG_1156
RPL35ALRG_1129
RPS7LRG_1148
RPS17LRG_1143
HGNC symbolLRG ID
SEC23BLRG_1134
SETBP1LRG_1150
SH3BP1LRG_1154
SLC25A38LRG_1133
SPTA1LRG_1131
SPTBLRG_1130
TBX4LRG_1206
THPOLRG_580
TJP2LRG_1201
UBE2TLRG_1169
VPS45LRG_1170
See more details here