NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) - NR_110737.1
 

RefSeq Gene LOC101928804


RefSeq: NR_110737.1  Status: Validated
Description: uncharacterized LOC101928804, transcript variant 1
Molecule type: ncRNA
Source: BestRefSeq
Biotype: lncRNA
Other notes: Mappings of the RefSeq transcript to different genomic sequences have varying alignment differences
Entrez Gene: 101928804
GeneCards: LOC101928804
AceView: LOC101928804

mRNA/Genomic Alignments (NR_110737.1)

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |   781  100.0%         19     -  54769422  54771064           NR_110737.1     1   781   781
browser |   781   99.5%  19_GL949746v1_alt     -    675083    676725           NR_110737.1     1   781   781
browser |   781  100.0%  19_GL949749v2_alt     -    841535    843177           NR_110737.1     1   781   781
browser |   781  100.0%  19_GL949751v2_alt     -    752258    753900           NR_110737.1     1   781   781
browser |   781  100.0%  19_GL949752v1_alt     -    673756    675398           NR_110737.1     1   781   781
browser |   781   99.7%  19_KI270882v1_alt     +    131687    133329           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270883v1_alt     +     97775     99417           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270885v1_alt     +     98344     99986           NR_110737.1     1   781   781
browser |   781   99.7%  19_KI270886v1_alt     +     87147     88790           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270887v1_alt     +    137361    139003           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270889v1_alt     +     98035     99677           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270891v1_alt     +     98051     99693           NR_110737.1     1   781   781
browser |   781   99.8%  19_KI270914v1_alt     +     87933     89575           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270915v1_alt     +     98035     99677           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270917v1_alt     -     48335     49977           NR_110737.1     1   781   781
browser |   781   99.9%  19_KI270918v1_alt     -     71000     72642           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270919v1_alt     +     98014     99656           NR_110737.1     1   781   781
browser |   781   99.5%  19_KI270920v1_alt     -     56262     57904           NR_110737.1     1   781   781
browser |   781   99.7%  19_KI270921v1_alt     -    112421    114063           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270922v1_alt     -     45336     46978           NR_110737.1     1   781   781
browser |   781   99.9%  19_KI270929v1_alt     -     43599     45241           NR_110737.1     1   781   781
browser |   781   99.7%  19_KI270930v1_alt     +     99527    101169           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270931v1_alt     +     97527     99169           NR_110737.1     1   781   781
browser |   781   99.3%  19_KI270932v1_alt     +     98383    100025           NR_110737.1     1   781   781
browser |   781   99.5%  19_KI270933v1_alt     +     97836     99478           NR_110737.1     1   781   781
browser |   781  100.0%  19_KI270938v1_alt     -    751988    753630           NR_110737.1     1   781   781
browser |   781  100.0%  19_KV575246v1_alt     -     71055     72697           NR_110737.1     1   781   781
browser |   781   99.5%  19_KV575247v1_alt     -     71063     72705           NR_110737.1     1   781   781
browser |   781   99.5%  19_KV575248v1_alt     -     71032     72674           NR_110737.1     1   781   781
browser |   781  100.0%  19_KV575249v1_alt     -     71000     72642           NR_110737.1     1   781   781
browser |   781   99.5%  19_KV575250v1_alt     -     71032     72674           NR_110737.1     1   781   781
browser |   781   99.5%  19_KV575251v1_alt     -     71019     72661           NR_110737.1     1   781   781
browser |   781   99.7%  19_KV575252v1_alt     -     70834     72477           NR_110737.1     1   781   781
browser |   781  100.0%  19_KV575253v1_alt     -     70989     72631           NR_110737.1     1   781   781
browser |   781  100.0%  19_KV575254v1_alt     -     71010     72652           NR_110737.1     1   781   781
browser |   781  100.0%  19_KV575255v1_alt     -     71029     72671           NR_110737.1     1   781   781
browser |   781   99.7%  19_KV575256v1_alt     -    101404    103046           NR_110737.1     1   781   781
browser |   781   99.5%  19_KV575257v1_alt     -     71023     72665           NR_110737.1     1   781   781
browser |   781   99.5%  19_KV575259v1_alt     -     71052     72694           NR_110737.1     1   781   781

View details of parts of alignment within browser window
.

Position: chr19:54769422-54771064
Band: 19q13.42
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_GL949746v1_alt:675083-676725
Band: 19_GL949746v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_GL949749v2_alt:841535-843177
Band: 19_GL949749v2_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_GL949751v2_alt:752258-753900
Band: 19_GL949751v2_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_GL949752v1_alt:673756-675398
Band: 19_GL949752v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KI270882v1_alt:131687-133329
Band: 19_KI270882v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270883v1_alt:97775-99417
Band: 19_KI270883v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270885v1_alt:98344-99986
Band: 19_KI270885v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270886v1_alt:87147-88790
Band: 19_KI270886v1_alt
Genomic Size: 1644
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270887v1_alt:137361-139003
Band: 19_KI270887v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270889v1_alt:98035-99677
Band: 19_KI270889v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270891v1_alt:98051-99693
Band: 19_KI270891v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270914v1_alt:87933-89575
Band: 19_KI270914v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270915v1_alt:98035-99677
Band: 19_KI270915v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270917v1_alt:48335-49977
Band: 19_KI270917v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KI270918v1_alt:71000-72642
Band: 19_KI270918v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KI270919v1_alt:98014-99656
Band: 19_KI270919v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270920v1_alt:56262-57904
Band: 19_KI270920v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KI270921v1_alt:112421-114063
Band: 19_KI270921v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KI270922v1_alt:45336-46978
Band: 19_KI270922v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KI270929v1_alt:43599-45241
Band: 19_KI270929v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KI270930v1_alt:99527-101169
Band: 19_KI270930v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270931v1_alt:97527-99169
Band: 19_KI270931v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270932v1_alt:98383-100025
Band: 19_KI270932v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270933v1_alt:97836-99478
Band: 19_KI270933v1_alt
Genomic Size: 1643
Strand: +
Gene Symbol: LOC101928804

Position: chr19_KI270938v1_alt:751988-753630
Band: 19_KI270938v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575246v1_alt:71055-72697
Band: 19_KV575246v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575247v1_alt:71063-72705
Band: 19_KV575247v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575248v1_alt:71032-72674
Band: 19_KV575248v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575249v1_alt:71000-72642
Band: 19_KV575249v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575250v1_alt:71032-72674
Band: 19_KV575250v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575251v1_alt:71019-72661
Band: 19_KV575251v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575252v1_alt:70834-72477
Band: 19_KV575252v1_alt
Genomic Size: 1644
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575253v1_alt:70989-72631
Band: 19_KV575253v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575254v1_alt:71010-72652
Band: 19_KV575254v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575255v1_alt:71029-72671
Band: 19_KV575255v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575256v1_alt:101404-103046
Band: 19_KV575256v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575257v1_alt:71023-72665
Band: 19_KV575257v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Position: chr19_KV575259v1_alt:71052-72694
Band: 19_KV575259v1_alt
Genomic Size: 1643
Strand: -
Gene Symbol: LOC101928804

Links to sequence:

View table schema

Go to NCBI RefSeq track controls

Data version: NCBI Homo sapiens Updated Annotation Release 109.20190905 (2019-09-10)
Data last updated: 2019-12-06

Description

The NCBI RefSeq Genes composite track shows human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences between the annotation coordinates provided by UCSC and NCBI. See the Methods section for more details about how the different tracks were created.

Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records.

For more information on the different gene tracks, see our Genes FAQ.

Display Conventions and Configuration

This track is a composite track that contains differing data sets. To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to hide. Note: Not all subtracts are available on all assemblies.

The subtracks available for this track include:
RefSeq aligned annotations and UCSC alignment of RefSeq annotations
  • RefSeq All – all curated and predicted annotations provided by RefSeq.
  • RefSeq Curated – subset of RefSeq All that includes only those annotations whose accessions begin with NM, NR, NP or YP. (NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.)
  • RefSeq Predicted – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.
  • RefSeq Other – all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks.
  • RefSeq Alignments – alignments of RefSeq RNAs to the human genome provided by the RefSeq group, following the display conventions for PSL tracks.
  • RefSeq Diffs – alignment differences between the human reference genome(s) and RefSeq transcripts. (Track not currently available for every assembly.)
  • RefSeq HGMD – only show RefSeq Curated transcripts annotated by the Human Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. It is the most restricted RefSeq subset, targeting clinical diagnostics.
  • RefSeq Select/MANE – only show transcript marked as RefSeq Select or MANE Select. A single Select transcript is chosen as representative for each protein-coding gene. Transcripts categorized as MANE are further agreed upon as representative by both NCBI RefSeq and Ensembl/GENCODE, and have a 100% identical match to a transcript in the Ensembl annotation. See NCBI RefSeq Select.
  • UCSC RefSeq – annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the human genome. This track was previously known as the "RefSeq Genes" track.

The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq Clinical, RefSeq Select/MANE and UCSC RefSeq tracks follow the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq.

Color Level of review
Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.
Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.
Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.

The item labels and codon display properties for features within this track can be configured through the check-box controls at the top of the track description page. To adjust the settings for an individual subtrack, click the wrench icon next to the track name in the subtrack list .

  • Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name or OMIM identifier instead of the gene name, show all or a subset of these labels including the gene name, OMIM identifier and accession names, or turn off the label completely.
  • Codon coloring: This track has an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.

The RefSeq Diffs track contains five different types of inconsistency between the reference genome sequence and the RefSeq transcript sequences. The five types of differences are as follows:

  • mismatch – aligned but mismatching bases, plus HGVS g. to show the genomic change required to match the transcript and HGVS c./n. to show the transcript change required to match the genome.
  • short gap – genomic gaps that are too small to be introns (arbitrary cutoff of < 45 bp), most likely insertions/deletion variants or errors, with HGVS g. and c./n. showing differences.
  • shift gap – shortGap items whose placement could be shifted left and/or right on the genome due to repetitive sequence, with HGVS c./n. position range of ambiguous region in transcript. Here, thin and thick lines are used -- the thin line shows the span of the repetitive sequence, and the thick line shows the rightmost shifted gap.
  • double gap – genomic gaps that are long enough to be introns but that skip over transcript sequence (invisible in default setting), with HGVS c./n. deletion.
  • skipped – sequence at the beginning or end of a transcript that is not aligned to the genome (invisible in default setting), with HGVS c./n. deletion
HGVS Terminology (Human Genome Variation Society): g. = genomic sequence ; c. = coding DNA sequence ; n. = non-coding RNA reference sequence.

When reporting HGVS with RefSeq sequences, to make sure that results from research articles can be mapped to the genome unambiguously, please specify the RefSeq annotation release displayed on the transcript's Genome Browser details page and also the RefSeq transcript ID with version (e.g. NM_012309.4 not NM_012309).

Methods

Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and converted to the genePred and PSL table formats for display in the Genome Browser. Information about the NCBI annotation pipeline can be found here.

The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments.

The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks. RefSeq RNAs were aligned against the human genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept.

Data Access

The raw data for these tracks can be accessed in multiple ways. It can be explored interactively using the Table Browser or Data Integrator. The tables can also be accessed programmatically through our public MySQL server or downloaded from our downloads server for local processing. You can also access any RefSeq table entries in JSON format through our JSON API.

The data in the RefSeq Other and RefSeq Diffs tracks are organized in bigBed file format; more information about accessing the information in this bigBed file can be found below. The other subtracks are associated with database tables as follows:

genePred format:
  • RefSeq All - ncbiRefSeq
  • RefSeq Curated - ncbiRefSeqCurated
  • RefSeq Predicted - ncbiRefSeqPredicted
  • RefSeq HGMD - ncbiRefSeqHgmd
  • RefSeq Select/MANE - ncbiRefSeqSelect
  • UCSC RefSeq - refGene
PSL format:
  • RefSeq Alignments - ncbiRefSeqPsl

The first column of each of these tables is "bin". This column is designed to speed up access for display in the Genome Browser, but can be safely ignored in downstream analysis. You can read more about the bin indexing system here.

The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed files, which can be obtained from our downloads server here, ncbiRefSeqOther.bb and ncbiRefSeqDiffs.bb. Individual regions or the whole set of genome-wide annotations can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system from the utilities directory linked below. For example, to extract only annotations in a given region, you could use the following command:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqOther.bb -chrom=chr16 -start=34990190 -end=36727467 stdout

You can download a GTF format version of the RefSeq All table from the GTF downloads directory. The genePred format tracks can also be converted to GTF format using the genePredToGtf utility, available from the utilities directory on the UCSC downloads server. The utility can be run from the command line like so:

genePredToGtf hg38 ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf

Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access section.

A file containing the RNA sequences in FASTA format for all items in the RefSeq All, RefSeq Curated, and RefSeq Predicted tracks can be found on our downloads server here.

Please refer to our mailing list archives for questions.

Credits

This track was produced at UCSC from data generated by scientists worldwide and curated by the NCBI RefSeq project.

References

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518

Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018

Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979