exRNAdisease

General Information

Database ID:

exR0000452

RNA Name:

AKIRIN2

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

87674860

End Site(bp):

87702233

External Links:

Disease Information

Disease Name:	Down Syndrome
Disease Category:	Congenital, Hereditary, and Neonatal Diseases and Abnormalities
MeSH ID:	D004314
Type:	Diseases Category/Congenital, Hereditary, and Neonatal Diseases and Abnormalities
Alias:	Syndrome, Down//Mongolism//47,XY,+21//Trisomy G//47,XX,+21//Down's Syndrome//Downs Syndrome//Syndrome, Down's//Trisomy 21//Trisomy 21, Mitotic Nondisjunction//Down Syndrome, Partial Trisomy 21//Partial Trisomy 21 Down Syndrome//Trisomy 21, Meiotic Nondisjunction

Expression Detail

GEO ID:	GSE16176
Description:	Expression profiles of amniotic fluid from human fetuses with Down syndrome and euploid controls
Experimental Design:	Disease vs Control
Case Disease Type:	Down Syndrome
Case Disease SubType:	NA
Case Sample:	Down Syndrome
Control Sample:	Normal
Number of Case:	7
Number of Control:	7
Number of Samples:	14

Regulatory Relationship

mRNA targets:

Gene Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
RPS27	chr1	153990762	153992155	+
PLCB3	chr11	64251523	64269150	+
TM9SF4	chr20	32109714	32167258	+
SLAIN2	chr4	48341529	48426201	+
COX4I1	chr16	85798633	85807068	+
FASN	chr17	82078338	82098294	-
ADGRL3	chr4	61201258	62078335	+
PITX1	chr5	135027734	135034813	-
RPLP0	chr12	120196699	120201235	-
KLC2	chr11	66257294	66267860	+
SOX4	chr6	21593751	21598619	+
UBE2Z	chr17	48908407	48929056	+
SMARCAL1	chr2	216412414	216483053	+
HCN1	chr5	45254948	45696498	-
HLA-DRA	chr6	32439878	32445046	+
SECISBP2	chr9	89318500	89359663	+
TAF7	chr5	141260225	141320784	-
ELOVL5	chr6	53267398	53349179	-
RPL18	chr19	48615328	48619184	-
UBC	chr12	124911604	124917368	-
SCAND1	chr20	35953617	35959472	-
TUBA1C	chr12	49188736	49274603	+
RACGAP1	chr12	49976923	50033136	-
ACTR10	chr14	58200080	58235636	+
HSP90AB1	chr6	44246166	44253888	+
AFTPH	chr2	64524305	64593005	+
EDARADD	chr1	236348257	236502915	+
UBE2Q2L	chr15	84172490	84182234	+
MFSD11	chr17	76735865	76781449	+
TP53	chr17	7661779	7687550	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-3648	chr21	8987026	8987046	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC079949.1	chr12	127142029	127146532	-
AL139819.1	chr10	100335563	100346390	-
RASAL2-AS1	chr1	178090677	178093984	-
SNHG25	chr17	64145970	64146476	+

Display:

Experiment Detail

GEO ID:	GSE16176
Sample Source:	Amniotic Fluid
Source Fraction:	Supernatant
Platform:	GPL570
Method:	Microarray
Num of detected RNA Type:	1
Num of detected RNAs of this Type:	17063
Sample treatment protocol:	NA
RNA Extract protocol:	RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer's protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
RNA library preparation protocol:	biotin Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

Reference

PMID:	19474297
Title:	Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses
Author:	Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW
Journal:	Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9425-9.
Description:	To characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we used Affymetrix microarrays to compare gene expression in uncultured amniotic fluid supernatant samples.