CSN1S1 (casein alpha s1) - Rat Genome Database

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Gene: CSN1S1 (casein alpha s1) Homo sapiens
Analyze
Symbol: CSN1S1
Name: casein alpha s1
RGD ID: 1606842
HGNC Page HGNC:2445
Description: Predicted to be involved in response to dehydroepiandrosterone; response to estradiol; and response to steroid hormone. Located in extracellular space.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: alpha-S1-casein; CASA; casein, alpha; CSN1; MGC149368
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38469,931,068 - 69,946,574 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl469,931,068 - 69,946,574 (+)EnsemblGRCh38hg38GRCh38
GRCh37470,796,786 - 70,812,292 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36470,831,388 - 70,846,877 (+)NCBINCBI36Build 36hg18NCBI36
Celera468,150,256 - 68,165,733 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef466,594,565 - 66,610,040 (+)NCBIHuRef
CHM1_1470,833,196 - 70,848,682 (+)NCBICHM1_1
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7556643   PMID:7619062   PMID:7665586   PMID:7698025   PMID:7790358   PMID:8192860   PMID:9050925   PMID:9820977   PMID:10971580   PMID:11329013   PMID:11827172   PMID:12477932  
PMID:12633878   PMID:12878203   PMID:16502470   PMID:16683014   PMID:17403899   PMID:18850735   PMID:20304780   PMID:20530684   PMID:20936779   PMID:21135174   PMID:21361910   PMID:21873635  
PMID:22474075   PMID:28514442   PMID:28786558   PMID:29884807   PMID:30945288   PMID:31067453   PMID:31594818   PMID:32296183   PMID:33961781  


Genomics

Comparative Map Data
CSN1S1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38469,931,068 - 69,946,574 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl469,931,068 - 69,946,574 (+)EnsemblGRCh38hg38GRCh38
GRCh37470,796,786 - 70,812,292 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36470,831,388 - 70,846,877 (+)NCBINCBI36Build 36hg18NCBI36
Celera468,150,256 - 68,165,733 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef466,594,565 - 66,610,040 (+)NCBIHuRef
CHM1_1470,833,196 - 70,848,682 (+)NCBICHM1_1
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBIT2T-CHM13v2.0
Csn1s1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39587,814,067 - 87,830,437 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl587,814,067 - 87,830,437 (+)EnsemblGRCm39 Ensembl
GRCm38587,666,208 - 87,682,578 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl587,666,208 - 87,682,578 (+)EnsemblGRCm38mm10GRCm38
MGSCv37588,095,249 - 88,111,599 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36588,740,785 - 88,757,135 (+)NCBIMGSCv36mm8
Celera585,369,865 - 85,382,927 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map543.56NCBI
Csn1s1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,622,858 - 20,638,849 (-)NCBIGRCr8
mRatBN7.21420,343,620 - 20,359,614 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,343,619 - 20,359,614 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,273,646 - 20,289,594 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,592,528 - 21,608,476 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,329,827 - 20,345,807 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,993,450 - 22,009,308 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,993,427 - 22,009,308 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,908,365 - 21,924,353 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,869,011 - 21,885,203 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,869,010 - 21,885,203 (-)NCBI
Celera1419,746,841 - 19,762,629 (-)NCBICelera
Cytogenetic Map14p21NCBI
Csn1s1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554472,908,095 - 2,928,444 (-)NCBIChiLan1.0ChiLan1.0
CSN1S1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2360,143,772 - 60,159,323 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1460,346,797 - 60,362,343 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0454,291,159 - 54,306,712 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1460,627,758 - 60,643,358 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl460,627,758 - 60,643,358 (-)Ensemblpanpan1.1panPan2
CSN1S1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11359,420,761 - 59,432,463 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1359,417,974 - 59,432,106 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1359,149,515 - 59,160,993 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01360,216,703 - 60,221,887 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11359,831,104 - 59,842,590 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01359,291,362 - 59,296,547 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01360,436,627 - 60,448,340 (+)NCBIUU_Cfam_GSD_1.0
Csn1s1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528516,269,217 - 16,279,920 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365984,710,875 - 4,735,033 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSN1S1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl866,888,231 - 66,907,913 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1866,888,231 - 66,908,306 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28148,201,997 - 148,222,498 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Csn1s1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248901,283,303 - 1,297,021 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CSN1S1
10 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q13.2-13.3(chr4:66842408-70831557)x1 copy number loss See cases [RCV000050704] Chr4:66842408..70831557 [GRCh38]
Chr4:67708126..71697274 [GRCh37]
Chr4:67390721..71916138 [NCBI36]
Chr4:4q13.2-13.3		 pathogenic
GRCh38/hg38 4q12-22.3(chr4:51831622-97505618)x3 copy number gain See cases [RCV000051772] Chr4:51831622..97505618 [GRCh38]
Chr4:52697788..98426769 [GRCh37]
Chr4:52392545..98645792 [NCBI36]
Chr4:4q12-22.3		 pathogenic
GRCh38/hg38 4q13.1-13.3(chr4:65454562-72313693)x1 copy number loss See cases [RCV000053293] Chr4:65454562..72313693 [GRCh38]
Chr4:66320280..73179410 [GRCh37]
Chr4:66002875..73398274 [NCBI36]
Chr4:4q13.1-13.3		 pathogenic
GRCh38/hg38 4q13.2-21.23(chr4:67869564-85517308)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053294]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053294]|See cases [RCV000053294] Chr4:67869564..85517308 [GRCh38]
Chr4:68735282..86438461 [GRCh37]
Chr4:68417877..86657485 [NCBI36]
Chr4:4q13.2-21.23		 pathogenic
GRCh38/hg38 4q13.3(chr4:69758599-70193037)x1 copy number loss See cases [RCV000054041] Chr4:69758599..70193037 [GRCh38]
Chr4:70624317..71058754 [GRCh37]
Chr4:70658906..71093343 [NCBI36]
Chr4:4q13.3		 uncertain significance
NM_001025104.1(CSN1S1):c.458C>T (p.Pro153Leu) single nucleotide variant Malignant melanoma [RCV000066499] Chr4:69944932 [GRCh38]
Chr4:70810650 [GRCh37]
Chr4:70845239 [NCBI36]
Chr4:4q13.3		 not provided
GRCh38/hg38 4q13.2-13.3(chr4:68902161-70620273)x3 copy number gain See cases [RCV000136751] Chr4:68902161..70620273 [GRCh38]
Chr4:69767879..71485990 [GRCh37]
Chr4:69802468..71520579 [NCBI36]
Chr4:4q13.2-13.3		 pathogenic
GRCh38/hg38 4q13.2-13.3(chr4:67799665-74240920)x1 copy number loss See cases [RCV000137622] Chr4:67799665..74240920 [GRCh38]
Chr4:68665383..75106637 [GRCh37]
Chr4:68347978..75325501 [NCBI36]
Chr4:4q13.2-13.3		 likely pathogenic
GRCh38/hg38 4q13.2-13.3(chr4:67744481-70267689)x1 copy number loss See cases [RCV000142366] Chr4:67744481..70267689 [GRCh38]
Chr4:68610199..71133406 [GRCh37]
Chr4:68292794..71167995 [NCBI36]
Chr4:4q13.2-13.3		 uncertain significance
GRCh38/hg38 4q13.3(chr4:69860680-70385052)x3 copy number gain See cases [RCV000143520] Chr4:69860680..70385052 [GRCh38]
Chr4:70726398..71250769 [GRCh37]
Chr4:70760987..71285358 [NCBI36]
Chr4:4q13.3		 likely benign|uncertain significance
GRCh38/hg38 4q13.2-22.3(chr4:68686088-95294456)x3 copy number gain See cases [RCV000143458] Chr4:68686088..95294456 [GRCh38]
Chr4:69551806..96215607 [GRCh37]
Chr4:69234401..96434630 [NCBI36]
Chr4:4q13.2-22.3		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:12440-190904441)x3 copy number gain See cases [RCV000446653] Chr4:12440..190904441 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4q13.1-21.1(chr4:66017575-76772947)x1 copy number loss See cases [RCV000510445] Chr4:66017575..76772947 [GRCh37]
Chr4:4q13.1-21.1		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473) copy number gain See cases [RCV000510453] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
NM_001890.2(CSN1S1):c.464T>A (p.Ile155Asn) single nucleotide variant not specified [RCV004299561] Chr4:69944911 [GRCh38]
Chr4:70810629 [GRCh37]
Chr4:4q13.3		 uncertain significance
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473)x3 copy number gain See cases [RCV000512241] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4q13.1-13.3(chr4:64705501-73469716)x3 copy number gain not provided [RCV000682409] Chr4:64705501..73469716 [GRCh37]
Chr4:4q13.1-13.3		 pathogenic
GRCh37/hg19 4q13.2-13.3(chr4:70012338-71167321)x3 copy number gain not provided [RCV000682416] Chr4:70012338..71167321 [GRCh37]
Chr4:4q13.2-13.3		 uncertain significance
GRCh37/hg19 4q13.3(chr4:70594519-70885440)x3 copy number gain not provided [RCV000682417] Chr4:70594519..70885440 [GRCh37]
Chr4:4q13.3		 uncertain significance
GRCh37/hg19 4q13.3(chr4:70725002-71237421)x3 copy number gain not provided [RCV000682418] Chr4:70725002..71237421 [GRCh37]
Chr4:4q13.3		 likely benign
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190915650)x3 copy number gain not provided [RCV000743155] Chr4:49450..190915650 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4q12-13.3(chr4:58332294-71587615)x1 copy number loss not provided [RCV000743602] Chr4:58332294..71587615 [GRCh37]
Chr4:4q12-13.3		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190963766)x3 copy number gain not provided [RCV000743156] Chr4:49450..190963766 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:11525-191028879)x3 copy number gain not provided [RCV000743147] Chr4:11525..191028879 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
NM_001890.2(CSN1S1):c.106-4G>T single nucleotide variant not provided [RCV000953500] Chr4:69935922 [GRCh38]
Chr4:70801640 [GRCh37]
Chr4:4q13.3		 likely benign
GRCh37/hg19 4q13.3(chr4:70618421-71083238)x1 copy number loss not provided [RCV001005554] Chr4:70618421..71083238 [GRCh37]
Chr4:4q13.3		 uncertain significance
GRCh37/hg19 4q13.2-21.22(chr4:68242784-82991431)x3 copy number gain not provided [RCV000845944] Chr4:68242784..82991431 [GRCh37]
Chr4:4q13.2-21.22		 pathogenic
NM_001890.2(CSN1S1):c.84+5A>G single nucleotide variant not provided [RCV000964119] Chr4:69934249 [GRCh38]
Chr4:70799967 [GRCh37]
Chr4:4q13.3		 benign
GRCh37/hg19 4q13.2-13.3(chr4:70478978-70985189)x1 copy number loss not provided [RCV002473768] Chr4:70478978..70985189 [GRCh37]
Chr4:4q13.2-13.3		 uncertain significance
GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1 copy number loss not provided [RCV001005553] Chr4:68950363..79738598 [GRCh37]
Chr4:4q13.2-21.21		 pathogenic
GRCh38/hg38 4q12-21.1(chr4:51891814-76009719)x1 copy number loss Piebaldism [RCV001420508] Chr4:51891814..76009719 [GRCh38]
Chr4:4q12-21.1		 pathogenic
GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3 copy number gain not provided [RCV001827738] Chr4:52866944..143582507 [GRCh37]
Chr4:4q12-31.21		 pathogenic
GRCh37/hg19 4q13.1-13.3(chr4:61867555-74711517) copy number loss not specified [RCV002053422] Chr4:61867555..74711517 [GRCh37]
Chr4:4q13.1-13.3		 pathogenic
NC_000004.12:g.67833055_82716065del deletion See cases [RCV003313802] Chr4:67833055..82716065 [GRCh38]
Chr4:4q13.2-21.22		 pathogenic
NM_001890.2(CSN1S1):c.496G>T (p.Asp166Tyr) single nucleotide variant not specified [RCV004204117] Chr4:69944943 [GRCh38]
Chr4:70810661 [GRCh37]
Chr4:4q13.3		 uncertain significance
GRCh37/hg19 4q13.2-13.3(chr4:70479061-70985189)x1 copy number loss not provided [RCV002475802] Chr4:70479061..70985189 [GRCh37]
Chr4:4q13.2-13.3		 uncertain significance
NM_001890.2(CSN1S1):c.544A>G (p.Met182Val) single nucleotide variant not specified [RCV004156905] Chr4:69944991 [GRCh38]
Chr4:70810709 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.199A>G (p.Thr67Ala) single nucleotide variant not specified [RCV004207898] Chr4:69937124 [GRCh38]
Chr4:70802842 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.529G>C (p.Glu177Gln) single nucleotide variant not specified [RCV004113065] Chr4:69944976 [GRCh38]
Chr4:70810694 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.541G>A (p.Val181Ile) single nucleotide variant not specified [RCV004228178] Chr4:69944988 [GRCh38]
Chr4:70810706 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.259A>G (p.Ile87Val) single nucleotide variant not specified [RCV004237105] Chr4:69939191 [GRCh38]
Chr4:70804909 [GRCh37]
Chr4:4q13.3		 uncertain significance
GRCh37/hg19 4q12-13.3(chr4:57584845-72430996)x1 copy number loss not provided [RCV003485417] Chr4:57584845..72430996 [GRCh37]
Chr4:4q12-13.3		 pathogenic
GRCh37/hg19 4q13.1-13.3(chr4:63684557-71480358)x3 copy number gain not provided [RCV003484182] Chr4:63684557..71480358 [GRCh37]
Chr4:4q13.1-13.3		 pathogenic
GRCh37/hg19 4q13.2-13.3(chr4:69146217-75500577)x1 copy number loss not provided [RCV003485422] Chr4:69146217..75500577 [GRCh37]
Chr4:4q13.2-13.3		 pathogenic
GRCh37/hg19 4q13.3(chr4:70563498-71253752)x1 copy number loss not specified [RCV003986514] Chr4:70563498..71253752 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.96G>C (p.Glu32Asp) single nucleotide variant not specified [RCV004372570] Chr4:69934701 [GRCh38]
Chr4:70800419 [GRCh37]
Chr4:4q13.3		 likely benign
NM_001890.2(CSN1S1):c.496G>A (p.Asp166Asn) single nucleotide variant not specified [RCV004372567] Chr4:69944943 [GRCh38]
Chr4:70810661 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.76C>T (p.Arg26Cys) single nucleotide variant not specified [RCV004372568] Chr4:69934236 [GRCh38]
Chr4:70799954 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.249G>A (p.Met83Ile) single nucleotide variant not specified [RCV004372565] Chr4:69939181 [GRCh38]
Chr4:70804899 [GRCh37]
Chr4:4q13.3		 uncertain significance
NM_001890.2(CSN1S1):c.88C>T (p.Pro30Ser) single nucleotide variant not specified [RCV004372569] Chr4:69934693 [GRCh38]
Chr4:70800411 [GRCh37]
Chr4:4q13.3		 uncertain significance
GRCh37/hg19 4p12-q35.2(chr4:45455621-191003541)x3 copy number gain not provided [RCV003885507] Chr4:45455621..191003541 [GRCh37]
Chr4:4p12-q35.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:696
Count of miRNA genes:197
Interacting mature miRNAs:203
Transcripts:ENST00000246891, ENST00000444405, ENST00000505782, ENST00000507763, ENST00000507772, ENST00000510936
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
RH91651  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37470,812,098 - 70,812,223UniSTSGRCh37
Build 36470,846,687 - 70,846,812RGDNCBI36
Celera468,165,543 - 68,165,668RGD
Cytogenetic Map4q21.1UniSTS
HuRef466,609,850 - 66,609,975UniSTS
GeneMap99-GB4 RH Map4411.84UniSTS
SHGC-68166  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37470,811,932 - 70,812,147UniSTSGRCh37
Build 36470,846,521 - 70,846,736RGDNCBI36
Celera468,165,377 - 68,165,592RGD
Cytogenetic Map4q21.1UniSTS
HuRef466,609,684 - 66,609,899UniSTS
GeneMap99-GB4 RH Map4421.24UniSTS
STS-X78416  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37470,811,963 - 70,812,220UniSTSGRCh37
Build 36470,846,552 - 70,846,809RGDNCBI36
Celera468,165,408 - 68,165,665RGD
Cytogenetic Map4q21.1UniSTS
HuRef466,609,715 - 66,609,972UniSTS
GeneMap99-GB4 RH Map4415.5UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage
High 1
Medium 5 5 1 2 212 10 2 1 284 6
Low 84 154 33 9 50 530 10 290 6 267 26 9 572 178
Below cutoff 602 825 348 162 481 59 1151 285 1004 50 266 304 104 239 819

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001025104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006714089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006714090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006714091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054348971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054348972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054348973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC108941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC128227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC128228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG217918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D85424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ064604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U23157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X78416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X98084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000246891   ⟹   ENSP00000246891
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl469,931,068 - 69,946,574 (+)Ensembl
RefSeq Acc Id: ENST00000505782   ⟹   ENSP00000426684
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl469,932,556 - 69,946,557 (+)Ensembl
RefSeq Acc Id: ENST00000507763   ⟹   ENSP00000422611
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl469,932,545 - 69,946,251 (+)Ensembl
RefSeq Acc Id: ENST00000507772   ⟹   ENSP00000427490
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl469,932,556 - 69,946,557 (+)Ensembl
RefSeq Acc Id: ENST00000510936   ⟹   ENSP00000421314
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl469,939,176 - 69,946,561 (+)Ensembl
RefSeq Acc Id: ENST00000633258   ⟹   ENSP00000487633
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl469,936,566 - 69,941,060 (+)Ensembl
RefSeq Acc Id: NM_001025104   ⟹   NP_001020275
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38469,931,068 - 69,946,574 (+)NCBI
GRCh37470,796,799 - 70,812,288 (+)ENTREZGENE
Build 36470,831,388 - 70,846,877 (+)NCBI Archive
HuRef466,594,565 - 66,610,040 (+)ENTREZGENE
CHM1_1470,833,196 - 70,848,682 (+)NCBI
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001890   ⟹   NP_001881
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38469,931,068 - 69,946,574 (+)NCBI
GRCh37470,796,799 - 70,812,288 (+)ENTREZGENE
Build 36470,831,388 - 70,846,877 (+)NCBI Archive
HuRef466,594,565 - 66,610,040 (+)ENTREZGENE
CHM1_1470,833,196 - 70,848,682 (+)NCBI
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006714089   ⟹   XP_006714152
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38469,931,068 - 69,946,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006714090   ⟹   XP_006714153
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38469,931,068 - 69,946,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006714091   ⟹   XP_006714154
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38469,931,068 - 69,946,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054348971   ⟹   XP_054204946
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBI
RefSeq Acc Id: XM_054348972   ⟹   XP_054204947
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBI
RefSeq Acc Id: XM_054348973   ⟹   XP_054204948
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0473,265,893 - 73,281,385 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001881   ⟸   NM_001890
- Peptide Label: isoform 1 precursor
- UniProtKB: E9PB60 (UniProtKB/Swiss-Prot),   A1A511 (UniProtKB/Swiss-Prot),   A1A510 (UniProtKB/Swiss-Prot),   Q4PNR5 (UniProtKB/Swiss-Prot),   P47710 (UniProtKB/Swiss-Prot),   E9PDQ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001020275   ⟸   NM_001025104
- Peptide Label: isoform 2 precursor
- UniProtKB: E9PDQ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006714153   ⟸   XM_006714090
- Peptide Label: isoform X2
- UniProtKB: D6RF34 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006714152   ⟸   XM_006714089
- Peptide Label: isoform X1
- UniProtKB: E9PDQ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006714154   ⟸   XM_006714091
- Peptide Label: isoform X3
- UniProtKB: D6RF34 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000426684   ⟸   ENST00000505782
RefSeq Acc Id: ENSP00000422611   ⟸   ENST00000507763
RefSeq Acc Id: ENSP00000427490   ⟸   ENST00000507772
RefSeq Acc Id: ENSP00000246891   ⟸   ENST00000246891
RefSeq Acc Id: ENSP00000421314   ⟸   ENST00000510936
RefSeq Acc Id: ENSP00000487633   ⟸   ENST00000633258
RefSeq Acc Id: XP_054204947   ⟸   XM_054348972
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054204946   ⟸   XM_054348971
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054204948   ⟸   XM_054348973
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P47710-F1-model_v2 AlphaFold P47710 1-185 view protein structure

Promoters
RGD ID:6867616
Promoter ID:EPDNEW_H6973
Type:single initiation site
Name:CSN1S1_1
Description:casein alpha s1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38469,931,068 - 69,931,128EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2445 AgrOrtholog
COSMIC CSN1S1 COSMIC
Ensembl Genes ENSG00000126545 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000246891 ENTREZGENE
  ENST00000246891.9 UniProtKB/Swiss-Prot
  ENST00000505782 ENTREZGENE
  ENST00000505782.5 UniProtKB/TrEMBL
  ENST00000507763 ENTREZGENE
  ENST00000507763.5 UniProtKB/Swiss-Prot
  ENST00000507772.5 UniProtKB/TrEMBL
  ENST00000510936.1 UniProtKB/TrEMBL
  ENST00000633258.1 UniProtKB/TrEMBL
GTEx ENSG00000126545 GTEx
HGNC ID HGNC:2445 ENTREZGENE
Human Proteome Map CSN1S1 Human Proteome Map
InterPro Alpha-s1_casein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Casein_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:1446 UniProtKB/Swiss-Prot
NCBI Gene 1446 ENTREZGENE
OMIM 115450 OMIM
PANTHER ALPHA-S1-CASEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10240 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA26948 PharmGKB
PROSITE CASEIN_ALPHA_BETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0J9YVR3_HUMAN UniProtKB/TrEMBL
  A1A510 ENTREZGENE
  A1A511 ENTREZGENE
  CASA1_HUMAN UniProtKB/Swiss-Prot
  D6RF34 ENTREZGENE, UniProtKB/TrEMBL
  E9PB60 ENTREZGENE
  E9PDQ1 ENTREZGENE, UniProtKB/TrEMBL
  H0Y8K1_HUMAN UniProtKB/TrEMBL
  P47710 ENTREZGENE
  Q4PNR5 ENTREZGENE
UniProt Secondary A1A510 UniProtKB/Swiss-Prot
  A1A511 UniProtKB/Swiss-Prot
  E9PB60 UniProtKB/Swiss-Prot
  Q4PNR5 UniProtKB/Swiss-Prot