AP001094.3 (novel transcript, antisense to PTPRM) - Rat Genome Database

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Gene: AP001094.3 (novel transcript, antisense to PTPRM) Homo sapiens
Analyze
Symbol: AP001094.3
Name: novel transcript, antisense to PTPRM
RGD ID: 16564195
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: PREDICTED
Previously known as: LOC100192426; uncharacterized LOC100192426
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38188,360,820 - 8,367,034 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl188,360,820 - 8,367,034 (-)EnsemblGRCh38hg38GRCh38
GRCh37188,360,818 - 8,367,032 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map18p11.23NCBI
HuRef188,325,248 - 8,331,462 (-)NCBIHuRef
CHM1_1188,360,999 - 8,367,213 (-)NCBICHM1_1
T2T-CHM13v2.0188,523,969 - 8,530,184 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:11181995  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 18p11.23(chr18:8293085-8402124)x3 copy number gain See cases [RCV000141098] Chr18:8293085..8402124 [GRCh38]
Chr18:8293083..8402122 [GRCh37]
Chr18:8283083..8392122 [NCBI36]
Chr18:18p11.23		 benign
GRCh38/hg38 18p11.31-11.22(chr18:6913068-9146867)x3 copy number gain See cases [RCV000142491] Chr18:6913068..9146867 [GRCh38]
Chr18:6913067..9146865 [GRCh37]
Chr18:6903067..9136865 [NCBI36]
Chr18:18p11.31-11.22		 uncertain significance
GRCh38/hg38 18p11.32-11.21(chr18:10001-15380684)x3 copy number gain See cases [RCV000052499] Chr18:10001..15380684 [GRCh38]
Chr18:10001..15380683 [GRCh37]
Chr18:1..15370683 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-q11.1(chr18:53345-20948503)x3 copy number gain See cases [RCV000052504] Chr18:53345..20948503 [GRCh38]
Chr18:53345..18528464 [GRCh37]
Chr18:43345..16782462 [NCBI36]
Chr18:18p11.32-q11.1		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:148963-10900517)x1 copy number loss See cases [RCV000137105] Chr18:148963..10900517 [GRCh38]
Chr18:148963..10900515 [GRCh37]
Chr18:138963..10890515 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:112259-14122522)x1 copy number loss See cases [RCV000053457] Chr18:112259..14122522 [GRCh38]
Chr18:112259..14122521 [GRCh37]
Chr18:102259..14112521 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:958974-11954935)x1 copy number loss See cases [RCV000142225] Chr18:958974..11954935 [GRCh38]
Chr18:958975..11954934 [GRCh37]
Chr18:948975..11944934 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:118760-80254946)x3 copy number gain See cases [RCV000138656] Chr18:118760..80254946 [GRCh38]
Chr18:118760..78012829 [GRCh37]
Chr18:108760..76113817 [NCBI36]
Chr18:18p11.32-q23		 pathogenic|conflicting data from submitters
GRCh38/hg38 18p11.31-11.21(chr18:3389362-14082029)x3 copy number gain See cases [RCV000052536] Chr18:3389362..14082029 [GRCh38]
Chr18:3389360..14082028 [GRCh37]
Chr18:3379360..14072028 [NCBI36]
Chr18:18p11.31-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:2425507-11904118)x3 copy number gain See cases [RCV000136590] Chr18:2425507..11904118 [GRCh38]
Chr18:2425506..11904117 [GRCh37]
Chr18:2415506..11894117 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:148963-13530126)x1 copy number loss See cases [RCV000053784] Chr18:148963..13530126 [GRCh38]
Chr18:148963..13530125 [GRCh37]
Chr18:138963..13520125 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:148963-14081888)x1 copy number loss See cases [RCV000051154] Chr18:148963..14081888 [GRCh38]
Chr18:148963..14081887 [GRCh37]
Chr18:138963..14071887 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80244381)x3 copy number gain See cases [RCV000052514] Chr18:148963..80244381 [GRCh38]
Chr18:148963..78002264 [GRCh37]
Chr18:138963..76103255 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000148072] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:148963-14081888)x1 copy number loss See cases [RCV000148129] Chr18:148963..14081888 [GRCh38]
Chr18:148963..14081887 [GRCh37]
Chr18:138963..14071887 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:118760-14089410)x4 copy number gain See cases [RCV000137456] Chr18:118760..14089410 [GRCh38]
Chr18:118760..14089409 [GRCh37]
Chr18:108760..14079409 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic|conflicting data from submitters
GRCh38/hg38 18p11.32-11.21(chr18:148963-13068104)x1 copy number loss See cases [RCV000053787] Chr18:148963..13068104 [GRCh38]
Chr18:148963..13068103 [GRCh37]
Chr18:138963..13058103 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:133157-14089410)x1 copy number loss See cases [RCV000138101] Chr18:133157..14089410 [GRCh38]
Chr18:133157..14089409 [GRCh37]
Chr18:123157..14079409 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:118760-12642431)x3 copy number gain See cases [RCV000143194] Chr18:118760..12642431 [GRCh38]
Chr18:118760..12642430 [GRCh37]
Chr18:108760..12632430 [NCBI36]
Chr18:18p11.32-11.21		 uncertain significance
GRCh38/hg38 18p11.32-11.21(chr18:136226-15198991)x4 copy number gain See cases [RCV000143434] Chr18:136226..15198991 [GRCh38]
Chr18:136226..15198990 [GRCh37]
Chr18:126226..15188990 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:136226-14337134)x3 copy number gain See cases [RCV000143477] Chr18:136226..14337134 [GRCh38]
Chr18:136226..14337133 [GRCh37]
Chr18:126226..14327133 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.22(chr18:131700-10536767)x1 copy number loss See cases [RCV000053781] Chr18:131700..10536767 [GRCh38]
Chr18:131700..10536764 [GRCh37]
Chr18:121700..10526764 [NCBI36]
Chr18:18p11.32-11.22		 pathogenic
GRCh38/hg38 18p11.31-11.22(chr18:7154668-10068356)x1 copy number loss See cases [RCV000053828] Chr18:7154668..10068356 [GRCh38]
Chr18:7154667..10068353 [GRCh37]
Chr18:7144667..10058353 [NCBI36]
Chr18:18p11.31-11.22		 pathogenic
GRCh38/hg38 18p11.23-11.21(chr18:7290175-13049470)x1 copy number loss See cases [RCV000137503] Chr18:7290175..13049470 [GRCh38]
Chr18:7290173..13049469 [GRCh37]
Chr18:7280173..13039469 [NCBI36]
Chr18:18p11.23-11.21		 likely pathogenic
GRCh38/hg38 18p11.32-q23(chr18:149089-80254936)x3 copy number gain See cases [RCV000139397] Chr18:149089..80254936 [GRCh38]
Chr18:149089..78012819 [GRCh37]
Chr18:139089..76113807 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:136226-15175006) copy number gain See cases [RCV000140442] Chr18:136226..15175006 [GRCh38]
Chr18:136226..15175005 [GRCh37]
Chr18:126226..15165005 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:148963-13715860)x1 copy number loss See cases [RCV000051027] Chr18:148963..13715860 [GRCh38]
Chr18:148963..13715859 [GRCh37]
Chr18:138963..13705859 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:118760-14089410)x1 copy number loss See cases [RCV000137457] Chr18:118760..14089410 [GRCh38]
Chr18:118760..14089409 [GRCh37]
Chr18:108760..14079409 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148763-80252290)x3 copy number gain See cases [RCV000052507] Chr18:148763..80252290 [GRCh38]
Chr18:148763..78010173 [GRCh37]
Chr18:138763..76111164 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.22(chr18:112259-9135777)x1 copy number loss See cases [RCV000053456] Chr18:112259..9135777 [GRCh38]
Chr18:112259..9135775 [GRCh37]
Chr18:102259..9125775 [NCBI36]
Chr18:18p11.32-11.22		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:131700-15121055)x1 copy number loss See cases [RCV000053458] Chr18:131700..15121055 [GRCh38]
Chr18:131700..15121054 [GRCh37]
Chr18:121700..15111054 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-q11.1(chr18:148963-21040153)x3 copy number gain See cases [RCV000052513] Chr18:148963..21040153 [GRCh38]
Chr18:148963..18620114 [GRCh37]
Chr18:138963..16874112 [NCBI36]
Chr18:18p11.32-q11.1		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:149089-80234391)x3 copy number gain See cases [RCV000134110] Chr18:149089..80234391 [GRCh38]
Chr18:149089..77992274 [GRCh37]
Chr18:139089..76093265 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:48782-14978076)x1 copy number loss See cases [RCV000141627] Chr18:48782..14978076 [GRCh38]
Chr18:48782..14978075 [GRCh37]
Chr18:38782..14968075 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:136226-80256240)x3 copy number gain See cases [RCV000143218] Chr18:136226..80256240 [GRCh38]
Chr18:136226..78014123 [GRCh37]
Chr18:126226..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.22(chr18:180229-10762632)x1 copy number loss See cases [RCV000136860] Chr18:180229..10762632 [GRCh38]
Chr18:180229..10762630 [GRCh37]
Chr18:170229..10752630 [NCBI36]
Chr18:18p11.32-11.22		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:53345-80209986)x3 copy number gain See cases [RCV000052501] Chr18:53345..80209986 [GRCh38]
Chr18:53345..77967869 [GRCh37]
Chr18:43345..76068860 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:1919684-15325188)x3 copy number gain See cases [RCV000052535] Chr18:1919684..15325188 [GRCh38]
Chr18:1919685..15325187 [GRCh37]
Chr18:1909685..15315187 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:131700-14226905)x1 copy number loss See cases [RCV000053461] Chr18:131700..14226905 [GRCh38]
Chr18:131700..14226904 [GRCh37]
Chr18:121700..14216904 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.22(chr18:118760-8999132)x1 copy number loss See cases [RCV000139022] Chr18:118760..8999132 [GRCh38]
Chr18:118760..8999130 [GRCh37]
Chr18:108760..8989130 [NCBI36]
Chr18:18p11.32-11.22		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:118760-15024003)x1 copy number loss See cases [RCV000141086] Chr18:118760..15024003 [GRCh38]
Chr18:118760..15024002 [GRCh37]
Chr18:108760..15014002 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:14316-14206225)x3 copy number gain See cases [RCV000141427] Chr18:14316..14206225 [GRCh38]
Chr18:14316..14206224 [GRCh37]
Chr18:4316..14196224 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:136227-80256240)x3 copy number gain See cases [RCV000142244] Chr18:136227..80256240 [GRCh38]
Chr18:136227..78014123 [GRCh37]
Chr18:126227..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:148963-14081888)x4 copy number gain See cases [RCV000135515] Chr18:148963..14081888 [GRCh38]
Chr18:148963..14081887 [GRCh37]
Chr18:138963..14071887 [NCBI36]
Chr18:18p11.32-11.21		 pathogenic
GRCh38/hg38 18p11.23-11.22(chr18:7542605-9320894)x3 copy number gain See cases [RCV000052538] Chr18:7542605..9320894 [GRCh38]
Chr18:7542603..9320892 [GRCh37]
Chr18:7532603..9310892 [NCBI36]
Chr18:18p11.23-11.22		 pathogenic
GRCh38/hg38 18p11.23(chr18:7438814-8412548)x3 copy number gain See cases [RCV000136985] Chr18:7438814..8412548 [GRCh38]
Chr18:7438812..8412546 [GRCh37]
Chr18:7428812..8402546 [NCBI36]
Chr18:18p11.23		 uncertain significance
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000051048] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-11.21(chr18:158286-14124574)x1 copy number loss Deletion of short arm of chromosome 18 [RCV003327630] Chr18:158286..14124574 [GRCh38]
Chr18:18p11.32-11.21		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:142
Interacting mature miRNAs:144
Transcripts:ENST00000580491
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.


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 1 1
Low 156 41 323 12 5 12 151 37 188 51 189 353 40 125
Below cutoff 848 925 796 196 198 135 2077 1012 1813 173 770 853 63 712 1347 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000580491
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl188,360,820 - 8,367,034 (-)Ensembl
RefSeq Acc Id: NR_024419
RefSeq Status: PREDICTED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38188,360,820 - 8,367,034 (-)NCBI
T2T-CHM13v2.0188,523,969 - 8,530,184 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein EAX01625 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC AP001094.3 COSMIC
Ensembl Genes ENSG00000266149 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000580491 ENTREZGENE
GTEx ENSG00000266149 GTEx
Human Proteome Map AP001094.3 Human Proteome Map
NCBI Gene LOC100192426 ENTREZGENE
RNAcentral URS000011E81B RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AP001094.3  novel transcript, antisense to PTPRM  LOC100192426  uncharacterized LOC100192426  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC100192426  uncharacterized LOC100192426  AP001094.3  novel transcript, antisense to PTPRM  Symbol and/or name change 5135510 APPROVED