LINC02055 (long intergenic non-protein coding RNA 2055) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: LINC02055 (long intergenic non-protein coding RNA 2055) Homo sapiens
Analyze
Symbol: LINC02055
Name: long intergenic non-protein coding RNA 2055
RGD ID: 11575259
HGNC Page HGNC
Description:
Type: ncrna
RefSeq Status: VALIDATED
Also known as: RP1130-1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8135,859,369 - 137,092,183 (+)EnsemblGRCh38hg38GRCh38
GRCh388136,530,798 - 136,897,601 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378137,543,041 - 137,909,844 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.23NCBI
CHM1_18137,542,242 - 138,126,922 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:27773892  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:353
Count of miRNA genes:271
Interacting mature miRNAs:282
Transcripts:ENST00000517345, ENST00000520060, ENST00000520068, ENST00000521034, ENST00000521090, ENST00000521097, ENST00000524346
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 1 1 6 1 4 5 1
Low 28 21 72 52 67 50 89 13 51 13 416 60 3 5 15 2
Below cutoff 1402 1318 1079 278 512 195 2019 954 2182 106 499 928 83 740 1237

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000502901
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,047,021 - 136,166,122 (+)Ensembl
RefSeq Acc Id: ENST00000517345
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,536,976 - 136,798,234 (+)Ensembl
RefSeq Acc Id: ENST00000520060
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,759 - 136,731,963 (+)Ensembl
RefSeq Acc Id: ENST00000520068
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,789,833 - 136,815,688 (+)Ensembl
RefSeq Acc Id: ENST00000521034
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,797,273 - 136,984,935 (+)Ensembl
RefSeq Acc Id: ENST00000521090
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,780,853 - 136,810,037 (+)Ensembl
RefSeq Acc Id: ENST00000521097
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,789,834 - 136,897,601 (+)Ensembl
RefSeq Acc Id: ENST00000523150
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,047,047 - 136,165,995 (+)Ensembl
RefSeq Acc Id: ENST00000523232
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,516,040 - 136,598,968 (+)Ensembl
RefSeq Acc Id: ENST00000524346
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,771 - 136,897,601 (+)Ensembl
RefSeq Acc Id: ENST00000648045
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8135,859,369 - 135,920,578 (+)Ensembl
RefSeq Acc Id: ENST00000648077
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,047,094 - 136,302,718 (+)Ensembl
RefSeq Acc Id: ENST00000649576
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,771 - 137,092,183 (+)Ensembl
RefSeq Acc Id: ENST00000650054
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8135,969,366 - 136,166,980 (+)Ensembl
RefSeq Acc Id: ENST00000650217
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8135,859,369 - 136,012,187 (+)Ensembl
RefSeq Acc Id: ENST00000650445
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,198,246 - 136,760,772 (+)Ensembl
RefSeq Acc Id: ENST00000650470
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,464,908 - 136,731,963 (+)Ensembl
RefSeq Acc Id: ENST00000650515
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,047,094 - 136,202,824 (+)Ensembl
RefSeq Acc Id: ENST00000653309
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,805,273 - 136,815,687 (+)Ensembl
RefSeq Acc Id: ENST00000654723
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,795 - 136,798,206 (+)Ensembl
RefSeq Acc Id: ENST00000655492
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,803 - 136,756,360 (+)Ensembl
RefSeq Acc Id: ENST00000658944
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,516,246 - 136,761,333 (+)Ensembl
RefSeq Acc Id: ENST00000659405
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,047,094 - 136,186,176 (+)Ensembl
RefSeq Acc Id: ENST00000660691
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,489,428 - 136,731,955 (+)Ensembl
RefSeq Acc Id: ENST00000662546
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,782 - 136,731,951 (+)Ensembl
RefSeq Acc Id: ENST00000663759
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,798 - 136,962,308 (+)Ensembl
RefSeq Acc Id: ENST00000663951
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,489,448 - 136,569,536 (+)Ensembl
RefSeq Acc Id: ENST00000664755
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,808 - 136,731,963 (+)Ensembl
RefSeq Acc Id: ENST00000666475
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,047,094 - 136,155,389 (+)Ensembl
RefSeq Acc Id: ENST00000667909
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,531,070 - 136,761,394 (+)Ensembl
RefSeq Acc Id: ENST00000669387
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,530,828 - 136,968,020 (+)Ensembl
RefSeq Acc Id: ENST00000671540
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8136,516,255 - 136,731,955 (+)Ensembl
RefSeq Acc Id: NR_147196
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388136,530,798 - 136,897,601 (+)NCBI
Sequence:
Promoters
RGD ID:15096293
Promoter ID:EPDNEWNC_H1109
Type:multiple initiation site
Name:LINC02055_1
Description:long intergenic non-protein coding RNA 2055 [Source:HGNCSymbol;Acc:HGNC:52895]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh388136,530,792 - 136,530,852EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3 copy number gain See cases [RCV000050638] Chr8:113580402..145054634 [GRCh38]
Chr8:114592631..146280020 [GRCh37]
Chr8:114661807..146250824 [NCBI36]
Chr8:8q23.3-24.3
pathogenic
GRCh38/hg38 8q24.21-24.3(chr8:128220912-145049449)x3 copy number gain See cases [RCV000050830] Chr8:128220912..145049449 [GRCh38]
Chr8:129233158..146274835 [GRCh37]
Chr8:129302340..146245639 [NCBI36]
Chr8:8q24.21-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:95606052-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|See cases [RCV000053677] Chr8:95606052..145054775 [GRCh38]
Chr8:96618280..146280161 [GRCh37]
Chr8:96687456..146250965 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000053678] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
GRCh38/hg38 8q24.21-24.23(chr8:126626164-137169427)x1 copy number loss See cases [RCV000054306] Chr8:126626164..137169427 [GRCh38]
Chr8:127638409..138181670 [GRCh37]
Chr8:127707591..138250852 [NCBI36]
Chr8:8q24.21-24.23
pathogenic
GRCh38/hg38 8q24.21-24.3(chr8:130115518-141228210)x3 copy number gain See cases [RCV000133621] Chr8:130115518..141228210 [GRCh38]
Chr8:131127764..142238309 [GRCh37]
Chr8:131196946..142307491 [NCBI36]
Chr8:8q24.21-24.3
pathogenic
GRCh38/hg38 8q24.23(chr8:136681023-136849939)x1 copy number loss See cases [RCV000136380] Chr8:136681023..136849939 [GRCh38]
Chr8:137693266..137862182 [GRCh37]
Chr8:137762448..137931364 [NCBI36]
Chr8:8q24.23
benign
GRCh38/hg38 8q24.13-24.3(chr8:124498498-145068712)x3 copy number gain See cases [RCV000137346] Chr8:124498498..145068712 [GRCh38]
Chr8:125510739..146294098 [GRCh37]
Chr8:125579920..146264902 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
GRCh38/hg38 8q24.22-24.3(chr8:130639182-145068712)x3 copy number gain See cases [RCV000137644] Chr8:130639182..145068712 [GRCh38]
Chr8:131651428..146294098 [GRCh37]
Chr8:131720610..146264902 [NCBI36]
Chr8:8q24.22-24.3
pathogenic|conflicting data from submitters
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q11.1-24.3(chr8:46031340-139285494)x3 copy number gain See cases [RCV000139539] Chr8:46031340..139285494 [GRCh38]
Chr8:46942962..140297737 [GRCh37]
Chr8:47062127..140366919 [NCBI36]
Chr8:8q11.1-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000148117] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
Single allele deletion Gestational diabetes mellitus uncontrolled [RCV000161553] Chr8:136667562..136845084 [GRCh38]
Chr8:137679805..137857327 [GRCh37]
Chr8:8q24.23
not provided
NC_000008.11:g.136675987_136845084del169098 deletion Normal pregnancy [RCV000161554] Chr8:136675987..136845084 [GRCh38]
Chr8:137688230..137857327 [GRCh37]
Chr8:8q24.23
not provided
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q21.3-24.23(chr8:86300584-137022587)x3 copy number gain See cases [RCV000135621] Chr8:86300584..137022587 [GRCh38]
Chr8:87312813..138034830 [GRCh37]
Chr8:87381929..138104012 [NCBI36]
Chr8:8q21.3-24.23
pathogenic|likely pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:103306336-145068712)x3 copy number gain See cases [RCV000142810] Chr8:103306336..145068712 [GRCh38]
Chr8:104318564..146294098 [GRCh37]
Chr8:104387740..146264902 [NCBI36]
Chr8:8q22.3-24.3
pathogenic|likely pathogenic
GRCh38/hg38 8q24.23(chr8:136675987-136845084)x1 copy number loss Normal pregnancy [RCV000161554]|Premature ovarian failure [RCV000225200] Chr8:136675987..136845084 [GRCh38]
Chr8:137688230..137857327 [GRCh37]
Chr8:8q24.23
pathogenic|benign|not provided

Additional Information

Database Acc Id Source(s)
COSMIC LINC02055 COSMIC
Ensembl Genes ENSG00000254101 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000524346 ENTREZGENE
GTEx ENSG00000254101 GTEx
HGNC ID HGNC:52895 ENTREZGENE
Human Proteome Map LINC02055 Human Proteome Map
NCBI Gene LINC02055 ENTREZGENE
RNAcentral URS000033D6AF RNACentral