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Rat Genome Information - RGSC Genome Assembly v6.0


The Norway rat is an important experimental model for many human disease, including arthritis, hypertension, diabetes, and cardiovascular diseases.

Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus; Rattus norvegicus.


Summary

AssemblyRGSC Genome Assembly v6.0
GCF_000001895.5
Total Sequence Length (bp)2,870,184,193
Total Ungapped Length (bp)2,729,985,504
Gaps Between Scaffolds (bp)440
Number of Scaffolds1,395
Scaffold N50 (bp)14,986,627
Scaffold L5065
Number of Contigs75,697
Contig N50 (bp)100,461
Contig L507,356
No. of NCBI chromosome records23

Gene Counts

Total Genes39373
Protein Coding genes22844
Non coding RNA8462
tRNA430
SnRNA1
rRNA5
Pseudogenes7609
miRNA Targets Confirmed93
miRNA Targets Predicted19567
Gene transcripts71880
Genes without orthologs21171
Genes with Orthologs18202

#Rat Genes with Orthologs in...

Human18011
Mouse17951
Chinchilla15908
Bonobo16844
Dog17084
Squirrel16228
Pig16891

Other

Exons334981
QTLS2289
SSLPs44873
Strains1950
ClinVar Variants56
Karyotype
 
Chromosomes
,
ChromosomeSequence LengthGap LengthGap CountContig CountRefSeq Id
1 282763074 14700753 7780 58 NC_005100.4
2 266435125 14197426 7138 46 NC_005101.4
3 177699992 7301159 4114 43 NC_005102.4
4 184226339 7221840 3914 28 NC_005103.4
5 173707219 7642474 4244 26 NC_005104.4
6 147991367 6165679 3474 24 NC_005105.4
7 145729302 6934126 4100 17 NC_005106.4
8 133307652 4774000 3152 26 NC_005107.4
9 122095297 5306378 2976 19 NC_005108.4
10 112626471 3039996 2538 17 NC_005109.4
11 90463843 3246769 1949 9 NC_005110.4
12 52716770 2892239 1941 13 NC_005111.4
13 114033958 5396487 2678 23 NC_005112.4
14 115493446 6014314 3013 18 NC_005113.4
15 111246239 5179110 2906 10 NC_005114.4
16 90668790 4501710 2398 15 NC_005115.4
17 90843779 3861880 2235 10 NC_005116.4
18 88201929 3659600 1957 7 NC_005117.4
19 62275575 2383999 1763 8 NC_005118.4
20 56205956 2147703 1549 13 NC_005119.4
X 159970021 13490321 6016 31 NC_005120.4
Y 3310458 121100 13 1 NC_024475.1
MT 16313 - - 1 NC_001665.2
Variants
ACI/EurMcwi (2019)
ACI/EurMcwi (MCW)
ACI/EurMcwi (RGD)
ACI/N (2020)
ACI/N (MCW)
BBDP/Wor (RGD)
BN-Lx/CubMcwi (2019)
BN/NHsdMcwi (2019)
BN/NHsdMcwi (2020)
BN/SsN (2020)
BN/SsN (MCW)
BUF/N (2020)
BXH2/CubMcwi (2020)
BXH3/CubMcwi (2020)
Buf/N (MCW)
COP/CrCrl (MCW & UW)
DA/OlaHsd (2019)
F344/DuCrl (2019)
F344/N (2020)
F344/NCrl (2019)
F344/NCrl (RGD)
F344/NRrrc (MCW)
F344/Stm (2019)
FHH/EurMcwi (2019)
FHH/EurMcwi (MCW)
FHH/EurMcwi (RGD)
FHL/EurMcwi (MCW)
FHL/EurMcwi (RGD)
FXLE16/Stm (2020)
FXLE18/Stm (2020)
GH/OmrMcwi (MCW)
GK/FarMcwi (2019)
GK/Ox (RGD)
HXB10/IpcvMcwi (2019)
HXB2/IpcvMcwi (2019)
HXB20/IpcvMcwi (2020)
HXB31/IpcvMcwi (2019)
HXB4/IpcvMcwi (2020)
LE/Stm (2019)
LE/Stm (RGD)
LEW/Crl (2019)
LEW/Crl (RGD)
LEW/NCrlBR (RGD)
LEXF10A/StmMcwi (2020)
LEXF11/Stm (2020)
LEXF1A/Stm (2019)
LEXF1C/Stm (2019)
LEXF2B/Stm (2019)
LEXF3/Stm (2020)
LEXF4/Stm (2020)
LH/MavRrrc (RGD)
LH/MavRrrcAek (2020)
LL/MavRrrc (RGD)
LL/MavRrrcAek (2020)
LN/MavRrrc (RGD)
LN/MavRrrcAek (2020)
M520/N (2020)
M520/N (MCW)
M520/NRrrcMcwi (2019)
MHS/Gib (RGD)
MNS/Gib (RGD)
MR/N (2020)
MR/N (MCW)
MWF/Hsd (2019)
PVG/Seac (2019)
SBH/Ygl (MCW)
SBH/Ygl (RGD)
SBN/Ygl (MCW)
SBN/Ygl (RGD)
SHR/NHsd (RGD)
SHR/OlalpcvMcwi (2019)
SHRSP/A3NCrl (2019)
SHRSP/Gcrc (RGD)
SR/JrHsd (2020)
SR/JrHsd (MCW)
SR/JrHsd (RGD)
SS/Jr (RGD)
SS/JrHsdMcwi (2019)
SS/JrHsdMcwi (MCW)
SS/JrHsdMcwi (RGD)
WAG/Rij (RGD)
WAG/RijCrl (2020)
WKY/Gcrc (RGD)
WKY/N (2020)
WKY/N (MCW)
WKY/NCrl (2019)
WKY/NCrl (RGD)
WKY/NHsd (RGD)
WN/N (2020)
WN/N (MCW)
SNV 5252616 4836257 3055496 5011873 3157538 2936904 1213912 1154246 1013217 1078401 121974 4698815 3330358 3294873 3043212 5035085 4995166 5010656 4747200 5019511 2982361 3130161 4984769 5058415 4536623 2970199 4250408 2860648 4652499 4812958 4622177 5284412 2947547 3446140 3662822 2742910 3543527 3592592 5097375 3083045 4449416 2576753 2476670 4820858 4813626 5089665 5052032 5066526 4681865 4790454 3009191 4833333 2969844 4717245 2972888 4675757 4700397 3162998 5001930 2846510 2879003 4758384 2973018 4884378 5020167 4586835 2986970 4272153 2920305 3342786 5468146 5364710 3271257 4750164 4693290 2985385 2833606 4902942 4404481 2905926 2717231 4424908 3392824 5230854 3411485 5499672 3265533 3140447 4772526 2928066
Ins 865579 - - 811797 - - 532141 524467 480104 496473 - 784504 674745 679015 - - 841877 846025 784133 843311 - - 841714 846176 - - - - 765581 800983 - 870997 - 715664 735457 623732 724096 686393 854546 - 798750 - - 792857 798791 854047 848284 847230 782246 784318 - 814775 - 788843 - 781504 776715 - 846826 - - 806700 - 834061 846851 - - - - - 885903 877039 - 801231 - - - 832540 - - - 762278 - 837279 - 893367 - - 799422 -
Del 1096040 - - 1020613 - - 739757 730012 665003 690376 - 987560 875175 878522 - - 1068081 1073704 987782 1070345 - - 1069540 1071599 - - - - 963461 1009152 - 1101456 - 933745 956259 816405 943514 878822 1082670 - 1023340 - - 996439 1005256 1081833 1076269 1073406 986752 986523 - 1028656 - 993112 - 986481 978274 - 1075804 - - 1020135 - 1059637 1072892 - - - - - 1114000 1103981 - 1013482 - - - 1056813 - - - 966272 - 1045796 - 1124098 - - 1009145 -
References