Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   

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
Base Pairs3,042,335,753
Total Sequence Length (bp)2,870,184,193
Total Assembly Gap Length (bp)140,198,789
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 Genes41276
Protein Coding genes23498
Non coding RNA8944
tRNA430
SnRNA1
rRNA5
Pseudogenes8309
miRNA Targets Confirmed93
miRNA Targets Predicted19693
Gene transcripts71879
Genes without orthologs23146
Genes with Orthologs18130

#Rat Genes with Orthologs in...

Human17896
Mouse17856
Chinchilla15883
Bonobo16586
Dog16851
Squirrel16037
Pig16906

Other

Exons334979
QTLS2270
SSLPs44831
Strains1769
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 (MCW)
ACI/EurMcwi (RGD)
ACI/N (MCW)
BBDP/Wor (RGD)
BN/SsN (MCW)
Buf/N (MCW)
COP/CrCrl (MCW & UW)
F344/NCrl (RGD)
F344/NRrrc (MCW)
FHH/EurMcwi (MCW)
FHH/EurMcwi (RGD)
FHL/EurMcwi (MCW)
FHL/EurMcwi (RGD)
GH/OmrMcwi (MCW)
GK/Ox (RGD)
LE/Stm (RGD)
LEW/Crl (RGD)
LEW/NCrlBR (RGD)
LH/MavRrrc (RGD)
LL/MavRrrc (RGD)
LN/MavRrrc (RGD)
M520/N (MCW)
MHS/Gib (RGD)
MNS/Gib (RGD)
MR/N (MCW)
SBH/Ygl (MCW)
SBH/Ygl (RGD)
SBN/Ygl (MCW)
SBN/Ygl (RGD)
SHR/NHsd (RGD)
SHRSP/Gcrc (RGD)
SR/JrHsd (MCW)
SR/JrHsd (RGD)
SS/Jr (RGD)
SS/JrHsdMcwi (MCW)
SS/JrHsdMcwi (RGD)
WAG/Rij (RGD)
WKY/Gcrc (RGD)
WKY/N (MCW)
WKY/NCrl (RGD)
WKY/NHsd (RGD)
WN/N (MCW)
SNV 4836257 3055496 3157538 2936904 121974 3043212 5035085 2982361 3130161 4536623 2970199 4250408 2860648 4622177 2947547 3083045 2576753 2476670 3009191 2969844 2972888 3162998 2846510 2879003 2973018 4586835 2986970 4272153 2920305 3342786 3271257 4693290 2985385 2833606 4404481 2905926 2717231 3392824 3411485 3265533 3140447 2928066
Ins - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Del - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
References

NHLBI Logo

RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.