AutismKB 2.0

Annotation Detail for SMC1A


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Basic Information Top
Gene Symbol:SMC1A ( CDLS2,DKFZp686L19178,DXS423E,KIAA0178,MGC138332,SB1.8,SMC1,SMC1L1,SMC1alpha,SMCB )
Gene Full Name: structural maintenance of chromosomes 1A
Band: Xp11.22
Quick LinksEntrez ID:8243; OMIM: 300040; Uniprot ID:SMC1A_HUMAN; ENSEMBL ID: ENSG00000072501; HGNC ID: 11111
Relate to Another Database: SFARIGene; denovo-db
Unigene EST Top
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
embryoid body6 / 7076184
blastocyst12 / 62319192
fetus43 / 56401276
neonate0 / 310970 
infant1 / 2362042
juvenile4 / 5555671
adult138 / 193912171
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adrenal tumor0 / 127940 
bladder carcinoma2 / 17475114
breast (mammary gland) tumor26 / 94178276
cervical tumor9 / 34366261
chondrosarcoma4 / 8282348
colorectal tumor12 / 114246105
esophageal tumor3 / 17290173
gastrointestinal tumor13 / 119369108
germ cell tumor43 / 263845162
glioma4 / 10688337
head and neck tumor16 / 136302117
kidney tumor12 / 68959174
leukemia9 / 9584293
liver tumor8 / 9635983
lung tumor10 / 10312796
lymphoma7 / 7175597
non-neoplasia4 / 9725041
normal231 / 336030768
ovarian tumor5 / 7668265
pancreatic tumor5 / 10461647
primitive neuroectodermal tumor of the CNS6 / 12568047
prostate cancer6 / 10268058
retinoblastoma6 / 46356129
skin tumor13 / 124949104
soft tissue/muscle tissue tumor14 / 125191111
uterine tumor11 / 90257121
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue0 / 131060 
adrenal gland1 / 3319730
ascites3 / 4001574
bladder6 / 29757201
blood4 / 12347832
bone3 / 7165541
bone marrow5 / 48801102
brain49 / 110098944
cervix9 / 48171186
connective tissue5 / 14925533
ear1 / 1621261
embryonic tissue23 / 215722106
esophagus3 / 20209148
eye22 / 211054104
heart4 / 8962644
intestine21 / 23447289
kidney20 / 21177794
larynx4 / 24145165
liver41 / 207743197
lung21 / 33697462
lymph2 / 4427045
lymph node19 / 91610207
mammary gland29 / 153271189
mouth12 / 67052178
muscle8 / 10771574
nerve1 / 1576863
ovary7 / 10205168
pancreas8 / 21481237
parathyroid1 / 2053948
pharynx0 / 413280 
pituitary gland2 / 16585120
placenta9 / 28082532
prostate11 / 18934558
salivary gland2 / 2015599
skin16 / 21057475
spleen5 / 5395292
stomach3 / 9661931
testis17 / 33044251
thymus3 / 8113136
thyroid0 / 474730 
tonsil0 / 169990 
trachea0 / 524130 
umbilical cord0 / 136800 
uterus26 / 232878111
vascular5 / 5178096
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 201589_at
Cell line Expression level Expression bar
721_B_lymphoblasts1363.15
Adipocyte13.85
AdrenalCortex16.2
Adrenalgland13.15
Amygdala19.3
Appendix15.2
AtrioventricularNode12.1
BDCA4+_DentriticCells310.5
Bonemarrow54.05
BronchialEpithelialCells56.75
CD105+_Endothelial596.85
CD14+_Monocytes196.8
CD19+_BCells(neg._sel.)104.9
CD33+_Myeloid519.1
CD34+596.05
CD4+_Tcells214.8
CD56+_NKCells234.8
CD71+_EarlyErythroid339.25
CD8+_Tcells225.45
CardiacMyocytes26.65
Caudatenucleus14.05
Cerebellum10.25
CerebellumPeduncles15
CiliaryGanglion11
CingulateCortex12.65
Colorectaladenocarcinoma197.1
DorsalRootGanglion11.75
FetalThyroid14.35
Fetalbrain12.7
Fetalliver207.95
Fetallung44.2
GlobusPallidus9.55
Heart20.6
Hypothalamus16.25
Kidney14.4
Leukemia_chronicMyelogenousK-562161.85
Leukemia_promyelocytic-HL-60159.85
Leukemialymphoblastic(MOLT-4)329.85
Liver20.2
Lung36.8
Lymphnode74.15
Lymphoma_burkitts(Daudi)188.75
Lymphoma_burkitts(Raji)35
MedullaOblongata12.15
OccipitalLobe11.1
OlfactoryBulb12.9
Ovary9.9
Pancreas16.7
PancreaticIslet15.2
ParietalLobe13.05
Pituitary20.85
Placenta112.65
Pons11.3
PrefrontalCortex19.1
Prostate46.6
Salivarygland13.6
SkeletalMuscle18.55
Skin11.8
SmoothMuscle23.05
Spinalcord20.55
SubthalamicNucleus10.8
SuperiorCervicalGanglion18.95
TemporalLobe12
Testis12.8
TestisGermCell10.7
TestisIntersitial11.45
TestisLeydigCell11.3
TestisSeminiferousTubule10.9
Thalamus14.5
Thymus257.3
Thyroid83.65
Tongue15.7
Tonsil29.7
Trachea30.75
TrigeminalGanglion15.45
Uterus80.25
UterusCorpus14.65
WholeBlood169.25
Wholebrain11.45
colon441.45
pineal_day76.04
pineal_night80.34
retina84.825
small_intestine398.9
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: A_23_P217411
  • Donor H0351.2001
  • Sex: Male     Age: 24 years     Race/Ethnicity: African American     Handedness: Left
  • Tissue Receipt Date: 7/29/2009     Serology: Pass      Tissue pH :6.72     Additional Medical Information :History of asthma
  • Postmortem Interval: 23 hours (estimated time of death to time that tissue is frozen)
  • Toxicology: Positive for atropine and caffeine, at levels usually not toxicologically significant
Tissue Expression(mean ± stddev) Expression Bar
Amygdala8.02 ± 0.25
Basal Forebrain8.38 ± 0.2
Basal Part of Pons7.62 ± 0.24
Cerebellar Cortex8.4 ± 0.19
Cerebellar Nuclei8.21 ± 0.38
Claustrum8.22 ± 0.41
Epithalamus8.56 ± 0.18
Frontal Lobe7.87 ± 0.34
Globus Pallidus8.44 ± 0.49
Hypothalamus7.79 ± 0.24
Insula7.76 ± 0.37
Limbic Lobe7.95 ± 0.43
Mesencephalon8.22 ± 0.34
Myelencephalon8.1 ± 0.41
Occipital Lobe8.48 ± 0.42
Parietal Lobe8.04 ± 0.31
Pontine Tegmentum8.11 ± 0.35
Striatum8.18 ± 0.51
Subthalamus7.8 ± 0.25
Temporal Lobe7.92 ± 0.29
Thalamus8.26 ± 0.22
White Matter9.21 ± 0.35
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Smc1aCBCerebellum10.57
11.31
Smc1aCTXCerebral cortex5.49
4.35
Smc1aHIPHippocampal region11.09
11.38
Smc1aHPFHippocampal formation8.82
8.69
Smc1aHYHypothalamus1.33
1.19
Smc1aLSXLateral septal complex1.07
1.25
Smc1aMBMidbrain3.74
3.76
Smc1aMYMedulla6.32
7.11
Smc1aOLFOlfactory bulb8
6.79
Smc1aPPons5.53
6.23
Smc1aPALPallidum1.83
1.83
Smc1aRHPRetrohippocampal region4.37
4.69
Smc1asAMYStriatum-like amygdalar nuclei0.61
0.46
Smc1aSTRStriatum1.19
1.12
Smc1aSTRdStriatum dorsal region0.8
0.87
Smc1aSTRvStriatum ventral region2.79
2.14
Smc1aTHThalamus2.11
1.95
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
PAp00005979 31 1091 1121 NSSAQAFLGPENPEEPYLDGINYNCVAPGKR Peptide Atlas
SMC1A_HUMAN_2 17 2 18 GFLKLIEIENFKSYKGR PRIDE
SMC1A_HUMAN_39 14 39 52 SNLMDAISFVLGEK PRIDE
SMC1A_HUMAN_700 12 700 711 QVQSQAHGLQMR PRIDE

Simple Query:


  (e.g. CHD8)

Syndromic Genes

Non-syndromic Genes

AutismKB Statistics

  • Studies: 1,036
  • Genes: 1,379
  • CNVs/SVs: 5,420
  • SNVs/Indels: 11,669
  • de novo Mutations: 5,669
  • Mosaics: 789
  • Linkage Regions: 172
  • Paper Collected: 6/30/2018
  • Last Update: 8/26/2018


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