AL133485.2 (novel transcript, antisense to NIN) - Rat Genome Database

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Gene: AL133485.2 (novel transcript, antisense to NIN) Homo sapiens
Analyze
Symbol: AL133485.2
Name: novel transcript, antisense to NIN
RGD ID: 16561880
Description: ASSOCIATED WITH genetic disease
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC105370489; uncharacterized LOC105370489
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381450,821,797 - 50,823,509 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1450,821,880 - 50,823,501 (+)EnsemblGRCh38hg38GRCh38
GRCh371451,288,515 - 51,290,227 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map14q22.1NCBI
CHM1_11451,227,049 - 51,228,761 (+)NCBICHM1_1
T2T-CHM13v2.01445,027,932 - 45,029,644 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Genomics

Variants

.
Variants in AL133485.2
17 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q22.1(chr14:50713909-50954844)x3 copy number gain See cases [RCV000052060] Chr14:50713909..50954844 [GRCh38]
Chr14:51180627..51421562 [GRCh37]
Chr14:50250377..50491312 [NCBI36]
Chr14:14q22.1		 uncertain significance
GRCh38/hg38 14q21.3-22.1(chr14:50091150-51777325)x3 copy number gain See cases [RCV000052059] Chr14:50091150..51777325 [GRCh38]
Chr14:50557868..52244043 [GRCh37]
Chr14:49627618..51313793 [NCBI36]
Chr14:14q21.3-22.1		 uncertain significance
GRCh38/hg38 14q21.1-22.3(chr14:39196172-56714461)x3 copy number gain See cases [RCV000140717] Chr14:39196172..56714461 [GRCh38]
Chr14:39665376..57181179 [GRCh37]
Chr14:38735127..56250932 [NCBI36]
Chr14:14q21.1-22.3		 likely pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q22.1-22.3(chr14:50591011-56286919)x1 copy number loss See cases [RCV000051519] Chr14:50591011..56286919 [GRCh38]
Chr14:51057729..56753637 [GRCh37]
Chr14:50127479..55823390 [NCBI36]
Chr14:14q22.1-22.3		 pathogenic
NM_020921.4(NIN):c.68C>T (p.Thr23Met) single nucleotide variant not provided [RCV003075571] Chr14:50821989 [GRCh38]
Chr14:51288707 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.139C>G (p.Pro47Ala) single nucleotide variant not provided [RCV002572717] Chr14:50821918 [GRCh38]
Chr14:51288636 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.35G>A (p.Arg12Gln) single nucleotide variant Inborn genetic diseases [RCV002983698] Chr14:50822022 [GRCh38]
Chr14:51288740 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.89A>C (p.Gln30Pro) single nucleotide variant not provided [RCV002917962] Chr14:50821968 [GRCh38]
Chr14:51288686 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.133G>A (p.Val45Met) single nucleotide variant Inborn genetic diseases [RCV002574116]|not provided [RCV002574117] Chr14:50821924 [GRCh38]
Chr14:51288642 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.102C>T (p.Thr34=) single nucleotide variant not provided [RCV002765489] Chr14:50821955 [GRCh38]
Chr14:51288673 [GRCh37]
Chr14:14q22.1		 likely benign
NM_020921.4(NIN):c.65C>T (p.Thr22Met) single nucleotide variant not provided [RCV002580606] Chr14:50821992 [GRCh38]
Chr14:51288710 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.10G>C (p.Val4Leu) single nucleotide variant Inborn genetic diseases [RCV003175692] Chr14:50822047 [GRCh38]
Chr14:51288765 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.104A>G (p.Asp35Gly) single nucleotide variant not provided [RCV003881246] Chr14:50821953 [GRCh38]
Chr14:51288671 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.57T>G (p.Ser19Arg) single nucleotide variant not provided [RCV003543332] Chr14:50822000 [GRCh38]
Chr14:51288718 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.66G>A (p.Thr22=) single nucleotide variant not provided [RCV003393428] Chr14:50821991 [GRCh38]
Chr14:51288709 [GRCh37]
Chr14:14q22.1		 likely benign
NM_020921.4(NIN):c.131A>T (p.Glu44Val) single nucleotide variant not provided [RCV003663486] Chr14:50821926 [GRCh38]
Chr14:51288644 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.183+14A>T single nucleotide variant not provided [RCV003878023] Chr14:50821860 [GRCh38]
Chr14:51288578 [GRCh37]
Chr14:14q22.1		 likely benign
NM_020921.4(NIN):c.134T>C (p.Val45Ala) single nucleotide variant not provided [RCV003663485] Chr14:50821923 [GRCh38]
Chr14:51288641 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.130G>A (p.Glu44Lys) single nucleotide variant not provided [RCV003851668] Chr14:50821927 [GRCh38]
Chr14:51288645 [GRCh37]
Chr14:14q22.1		 uncertain significance
NM_020921.4(NIN):c.183+20G>A single nucleotide variant not provided [RCV003869525] Chr14:50821854 [GRCh38]
Chr14:51288572 [GRCh37]
Chr14:14q22.1		 likely benign
NM_020921.4(NIN):c.97C>G (p.Leu33Val) single nucleotide variant not provided [RCV003707256] Chr14:50821960 [GRCh38]
Chr14:51288678 [GRCh37]
Chr14:14q22.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:135
Interacting mature miRNAs:138
Transcripts:ENST00000555966
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 3 336
Low 17 212 15 1 621 114 13 48 8 53 48 2 10 76 1
Below cutoff 248 549 195 52 617 31 650 166 687 56 142 279 27 172 371 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000555966
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1450,821,880 - 50,823,501 (+)Ensembl
RefSeq Acc Id: NR_135258
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381450,821,797 - 50,823,509 (+)NCBI
T2T-CHM13v2.01445,027,932 - 45,029,644 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AL133485.2 COSMIC
Ensembl Genes ENSG00000258843 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000555966 ENTREZGENE
GTEx ENSG00000258843 GTEx
Human Proteome Map AL133485.2 Human Proteome Map
NCBI Gene LOC105370489 ENTREZGENE
RNAcentral URS0000A76C3E RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AL133485.2  novel transcript, antisense to NIN  LOC105370489  uncharacterized LOC105370489  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC105370489  uncharacterized LOC105370489  AL133485.2  novel transcript, antisense to NIN  Symbol and/or name change 5135510 APPROVED