AKT3-IT1 (AKT3 intronic transcript 1) - Rat Genome Database

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Gene: AKT3-IT1 (AKT3 intronic transcript 1) Homo sapiens
Analyze
Symbol: AKT3-IT1
Name: AKT3 intronic transcript 1
RGD ID: 6481089
HGNC Page HGNC:41304
Description: ASSOCIATED WITH Megalencephaly-Polymicrogyria-Polydactyly-Hydrocephalus Syndrome 2; Senior-Loken Syndrome 7
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381243,793,205 - 243,794,400 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1243,793,205 - 243,794,400 (-)EnsemblGRCh38hg38GRCh38
GRCh371243,956,507 - 243,957,702 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q44NCBI
T2T-CHM13v2.01243,204,335 - 243,205,531 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q41-44(chr1:223815147-248918469)x3 copy number gain See cases [RCV000135839] Chr1:223815147..248918469 [GRCh38]
Chr1:224002849..249212668 [GRCh37]
Chr1:222069472..247179291 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241676908-245647727)x1 copy number loss See cases [RCV000054027] Chr1:241676908..245647727 [GRCh38]
Chr1:241840210..245811029 [GRCh37]
Chr1:239906833..243877652 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239629868-248924593)x1 copy number loss See cases [RCV000054024] Chr1:239629868..248924593 [GRCh38]
Chr1:239793168..249218792 [GRCh37]
Chr1:237859791..247185415 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242240797-245200164)x1 copy number loss See cases [RCV000054030] Chr1:242240797..245200164 [GRCh38]
Chr1:242404099..245363466 [GRCh37]
Chr1:240470722..243430089 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243145749-244433395)x1 copy number loss See cases [RCV000142668] Chr1:243145749..244433395 [GRCh38]
Chr1:243309051..244596697 [GRCh37]
Chr1:241375674..242663320 [NCBI36]
Chr1:1q43-44		 pathogenic|likely benign|uncertain significance
GRCh38/hg38 1q43-44(chr1:237906379-244022201)x1 copy number loss See cases [RCV000053990] Chr1:237906379..244022201 [GRCh38]
Chr1:238069679..244185503 [GRCh37]
Chr1:236136302..242252126 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241047422-248924593)x1 copy number loss See cases [RCV000054025] Chr1:241047422..248924593 [GRCh38]
Chr1:241210722..249218792 [GRCh37]
Chr1:239277345..247185415 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242932576-248864636)x4 copy number gain See cases [RCV000137155] Chr1:242932576..248864636 [GRCh38]
Chr1:243095878..249158835 [GRCh37]
Chr1:241162501..247125458 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243225391-245289313)x1 copy number loss See cases [RCV000054032] Chr1:243225391..245289313 [GRCh38]
Chr1:243388693..245452615 [GRCh37]
Chr1:241455316..243519238 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.11-44(chr1:224022862-248918469)x3 copy number gain See cases [RCV000137769] Chr1:224022862..248918469 [GRCh38]
Chr1:224210564..249212668 [GRCh37]
Chr1:222277187..247179291 [NCBI36]
Chr1:1q42.11-44		 pathogenic
GRCh38/hg38 1q44(chr1:243677224-244923447)x1 copy number loss See cases [RCV000050929] Chr1:243677224..244923447 [GRCh38]
Chr1:243840526..245086749 [GRCh37]
Chr1:241907149..243153372 [NCBI36]
Chr1:1q44		 pathogenic
GRCh38/hg38 1q32.3-44(chr1:214023812-248918469)x3 copy number gain See cases [RCV000050981] Chr1:214023812..248918469 [GRCh38]
Chr1:214197155..249212668 [GRCh37]
Chr1:212263778..247179291 [NCBI36]
Chr1:1q32.3-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238351121-248918469)x1 copy number loss See cases [RCV000134172] Chr1:238351121..248918469 [GRCh38]
Chr1:238514421..249212668 [GRCh37]
Chr1:236581044..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223887780-248891309)x3 copy number gain See cases [RCV000051880] Chr1:223887780..248891309 [GRCh38]
Chr1:224075482..249185508 [GRCh37]
Chr1:222142105..247152131 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:240244444-248891309)x3 copy number gain See cases [RCV000051888] Chr1:240244444..248891309 [GRCh38]
Chr1:240407744..249185508 [GRCh37]
Chr1:238474367..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238033575-248924534)x1 copy number loss See cases [RCV000140039] Chr1:238033575..248924534 [GRCh38]
Chr1:238196875..249218733 [GRCh37]
Chr1:236263498..247185356 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.11-44(chr1:224096488-248918469)x3 copy number gain See cases [RCV000051882] Chr1:224096488..248918469 [GRCh38]
Chr1:224284190..249212668 [GRCh37]
Chr1:222350813..247179291 [NCBI36]
Chr1:1q42.11-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238753749-248918467)x1 copy number loss See cases [RCV000134751] Chr1:238753749..248918467 [GRCh38]
Chr1:238917049..249212666 [GRCh37]
Chr1:236983672..247179289 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242782194-245138126)x3 copy number gain See cases [RCV000140438] Chr1:242782194..245138126 [GRCh38]
Chr1:242945496..245301428 [GRCh37]
Chr1:241012119..243368051 [NCBI36]
Chr1:1q43-44		 uncertain significance
GRCh38/hg38 1q43-44(chr1:241757249-248891309)x1 copy number loss See cases [RCV000054028] Chr1:241757249..248891309 [GRCh38]
Chr1:241920551..249185508 [GRCh37]
Chr1:239987174..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q44(chr1:243786629-248918469)x1 copy number loss See cases [RCV000054061] Chr1:243786629..248918469 [GRCh38]
Chr1:243949931..249212668 [GRCh37]
Chr1:242016554..247179291 [NCBI36]
Chr1:1q44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241459440-247704671)x1 copy number loss See cases [RCV000054026] Chr1:241459440..247704671 [GRCh38]
Chr1:241622740..247867973 [GRCh37]
Chr1:239689363..245934596 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.12-44(chr1:225438480-248787200)x3 copy number gain See cases [RCV000142448] Chr1:225438480..248787200 [GRCh38]
Chr1:225626182..249060210 [GRCh37]
Chr1:223692805..247048022 [NCBI36]
Chr1:1q42.12-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238192880-248930485)x1 copy number loss See cases [RCV000143374] Chr1:238192880..248930485 [GRCh38]
Chr1:238356180..249224684 [GRCh37]
Chr1:236422803..247191307 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.13-44(chr1:229022909-248918469)x3 copy number gain See cases [RCV000136666] Chr1:229022909..248918469 [GRCh38]
Chr1:229158656..249212668 [GRCh37]
Chr1:227225279..247179291 [NCBI36]
Chr1:1q42.13-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241967139-245542967)x3 copy number gain See cases [RCV000138233] Chr1:241967139..245542967 [GRCh38]
Chr1:242130441..245706269 [GRCh37]
Chr1:240197064..243772892 [NCBI36]
Chr1:1q43-44		 likely pathogenic
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3 copy number gain See cases [RCV000143727] Chr1:207346642..248930485 [GRCh38]
Chr1:207519987..249224684 [GRCh37]
Chr1:205586610..247191307 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:236556082-248918469)x1 copy number loss See cases [RCV000137554] Chr1:236556082..248918469 [GRCh38]
Chr1:236719382..249212668 [GRCh37]
Chr1:234786005..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3 copy number gain See cases [RCV000051861] Chr1:209646207..248931113 [GRCh38]
Chr1:209819552..249225312 [GRCh37]
Chr1:207886175..247191935 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3 copy number gain See cases [RCV000134979] Chr1:209963625..248918469 [GRCh38]
Chr1:210136970..249212668 [GRCh37]
Chr1:208203593..247179291 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242045279-248930485)x1 copy number loss See cases [RCV000139889] Chr1:242045279..248930485 [GRCh38]
Chr1:242208581..249224684 [GRCh37]
Chr1:240275204..247191307 [NCBI36]
Chr1:1q43-44		 pathogenic
Single allele deletion Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 [RCV000235042] Chr1:242100310..244396371 [GRCh38]
Chr1:242263612..244559673 [GRCh37]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:240465122-248918469)x1 copy number loss See cases [RCV000137260] Chr1:240465122..248918469 [GRCh38]
Chr1:240628422..249212668 [GRCh37]
Chr1:238695045..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242828731-248891309)x3 copy number gain See cases [RCV000053504] Chr1:242828731..248891309 [GRCh38]
Chr1:242992033..249185508 [GRCh37]
Chr1:241058656..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239558430-248918469)x1 copy number loss See cases [RCV000054023] Chr1:239558430..248918469 [GRCh38]
Chr1:239721730..249212668 [GRCh37]
Chr1:237788353..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242410569-245413313)x1 copy number loss See cases [RCV000054031] Chr1:242410569..245413313 [GRCh38]
Chr1:242573871..245576615 [GRCh37]
Chr1:240640494..243643238 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241625115-245453782)x3 copy number gain See cases [RCV000136503] Chr1:241625115..245453782 [GRCh38]
Chr1:241788417..245617084 [GRCh37]
Chr1:239855040..243683707 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243264192-244668463)x1 copy number loss See cases [RCV000134045] Chr1:243264192..244668463 [GRCh38]
Chr1:243427494..244831765 [GRCh37]
Chr1:241494117..242898388 [NCBI36]
Chr1:1q43-44		 pathogenic
NC_000001.11:g.(?_242268256)_(243843190_?)del deletion Senior-Loken syndrome 7 [RCV000817924] Chr1:242268256..243843190 [GRCh38]
Chr1:242431558..244006492 [GRCh37]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223347693-248918469)x3 copy number gain See cases [RCV000050581] Chr1:223347693..248918469 [GRCh38]
Chr1:223521035..249212668 [GRCh37]
Chr1:221587658..247179291 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q44(chr1:243786629-243870496)x1 copy number loss See cases [RCV000134209] Chr1:243786629..243870496 [GRCh38]
Chr1:243949931..244033798 [GRCh37]
Chr1:242016554..242100421 [NCBI36]
Chr1:1q44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223828500-248891309)x3 copy number gain See cases [RCV000051878] Chr1:223828500..248891309 [GRCh38]
Chr1:224016202..249185508 [GRCh37]
Chr1:222082825..247152131 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:237643281-248918469)x1 copy number loss See cases [RCV000142518] Chr1:237643281..248918469 [GRCh38]
Chr1:237806581..249212668 [GRCh37]
Chr1:235873204..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243304751-244019666)x3 copy number gain See cases [RCV000142682] Chr1:243304751..244019666 [GRCh38]
Chr1:243468053..244182968 [GRCh37]
Chr1:241534676..242249591 [NCBI36]
Chr1:1q43-44		 uncertain significance
GRCh38/hg38 1q43-44(chr1:242164274-245299473)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327716] Chr1:242164274..245299473 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243221458-248919110)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327711] Chr1:243221458..248919110 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.3-44(chr1:235215476-247005888)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327725] Chr1:235215476..247005888 [GRCh38]
Chr1:1q42.3-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242520315-246857912)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003333898] Chr1:242520315..246857912 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239907336-248919110)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003333897] Chr1:239907336..248919110 [GRCh38]
Chr1:1q43-44		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:146
Count of miRNA genes:144
Interacting mature miRNAs:146
Transcripts:ENST00000417120
Prediction methods:Miranda, Rnahybrid
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.


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 entire extraembryonic component
High
Medium 1 3 6 3
Low 113 152 129 8 245 8 321 71 466 57 262 223 3 81 202 3
Below cutoff 1246 1237 865 141 547 90 2067 918 2085 160 779 874 53 732 1247 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000417120
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1243,793,205 - 243,794,400 (-)Ensembl
RefSeq Acc Id: NR_046761
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381243,793,205 - 243,794,400 (-)NCBI
T2T-CHM13v2.01243,204,335 - 243,205,531 (-)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC AKT3-IT1 COSMIC
Ensembl Genes ENSG00000228939 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000417120 ENTREZGENE
GTEx ENSG00000228939 GTEx
HGNC ID HGNC:41304 ENTREZGENE
Human Proteome Map AKT3-IT1 Human Proteome Map
NCBI Gene AKT3-IT1 ENTREZGENE
RNAcentral URS00002C213E RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-03 AKT3-IT1  AKT3 intronic transcript 1    AKT3 intronic transcript 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED