AL450226.1 (novel transcript, antisense to SMG6) - Rat Genome Database

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Gene: AL450226.1 (novel transcript, antisense to SMG6) Homo sapiens
Analyze
Symbol: AL450226.1
Name: novel transcript, antisense to SMG6
RGD ID: 16553082
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC101927839; uncharacterized LOC101927839
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38172,232,678 - 2,233,610 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl172,232,680 - 2,233,610 (+)EnsemblGRCh38hg38GRCh38
GRCh37172,135,972 - 2,136,904 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17p13.3NCBI
HuRef172,030,717 - 2,031,866 (+)NCBIHuRef
CHM1_1172,144,554 - 2,145,703 (+)NCBICHM1_1
T2T-CHM13v2.0172,119,929 - 2,120,861 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17p13.3(chr17:436763-2527511)x3 copy number gain See cases [RCV000052432] Chr17:436763..2527511 [GRCh38]
Chr17:396627..2430805 [GRCh37]
Chr17:286785..2377555 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:1287199-3154232)x3 copy number gain See cases [RCV000052448] Chr17:1287199..3154232 [GRCh38]
Chr17:1190493..3057526 [GRCh37]
Chr17:1137243..3004276 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:237248-4735533)x1 copy number loss See cases [RCV000141559] Chr17:237248..4735533 [GRCh38]
Chr17:396627..4638828 [GRCh37]
Chr17:87039..4585577 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:150732-5935377)x1 copy number loss See cases [RCV000141658] Chr17:150732..5935377 [GRCh38]
Chr17:525..5838697 [GRCh37]
Chr17:525..5779421 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3(chr17:198748-2261786)x1 copy number loss See cases [RCV000051148] Chr17:198748..2261786 [GRCh38]
Chr17:50690..2165080 [GRCh37]
Chr17:48539..2111830 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:162016-7697012)x1 copy number loss See cases [RCV000138214] Chr17:162016..7697012 [GRCh38]
Chr17:45835..7600330 [GRCh37]
Chr17:11807..7541055 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3-12(chr17:150732-14764202)x3 copy number gain See cases [RCV000142236] Chr17:150732..14764202 [GRCh38]
Chr17:525..14667519 [GRCh37]
Chr17:525..14608244 [NCBI36]
Chr17:17p13.3-12		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:198748-4265640)x1 copy number loss See cases [RCV000142440] Chr17:198748..4265640 [GRCh38]
Chr17:50690..4168935 [GRCh37]
Chr17:48539..4115684 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:2062380-5258340)x1 copy number loss See cases [RCV000133721] Chr17:2062380..5258340 [GRCh38]
Chr17:1965674..5161635 [GRCh37]
Chr17:1912424..5102359 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3(chr17:198748-3102332)x1 copy number loss See cases [RCV000050936] Chr17:198748..3102332 [GRCh38]
Chr17:50690..3005626 [GRCh37]
Chr17:48539..2952376 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:1065649-2261786)x1 copy number loss See cases [RCV000050815] Chr17:1065649..2261786 [GRCh38]
Chr17:968889..2165080 [GRCh37]
Chr17:915639..2111830 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:162088-6959050)x1 copy number loss See cases [RCV000134135] Chr17:162088..6959050 [GRCh38]
Chr17:45835..6862369 [GRCh37]
Chr17:11879..6803093 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3(chr17:1227392-2261993)x1 copy number loss See cases [RCV000138512] Chr17:1227392..2261993 [GRCh38]
Chr17:1130686..2165287 [GRCh37]
Chr17:1077436..2112037 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:1742705-2952264)x1 copy number loss See cases [RCV000138203] Chr17:1742705..2952264 [GRCh38]
Chr17:1645999..2855558 [GRCh37]
Chr17:1592749..2802308 [NCBI36]
Chr17:17p13.3		 pathogenic|likely benign
GRCh38/hg38 17p13.3(chr17:1808796-2403389)x3 copy number gain See cases [RCV000139433] Chr17:1808796..2403389 [GRCh38]
Chr17:1712090..2306683 [GRCh37]
Chr17:1658840..2253433 [NCBI36]
Chr17:17p13.3		 pathogenic|uncertain significance
GRCh38/hg38 17p13.3(chr17:445331-2385512)x3 copy number gain See cases [RCV000052434] Chr17:445331..2385512 [GRCh38]
Chr17:396627..2288806 [GRCh37]
Chr17:295350..2235556 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:1348488-3513273)x3 copy number gain See cases [RCV000137603] Chr17:1348488..3513273 [GRCh38]
Chr17:1251782..3416567 [GRCh37]
Chr17:1198532..3363317 [NCBI36]
Chr17:17p13.3-13.2		 likely pathogenic
GRCh38/hg38 17p13.3(chr17:198748-2685361)x1 copy number loss See cases [RCV000134971] Chr17:198748..2685361 [GRCh38]
Chr17:50690..2588655 [GRCh37]
Chr17:48539..2535405 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:2062429-4141883)x3 copy number gain See cases [RCV000139738] Chr17:2062429..4141883 [GRCh38]
Chr17:1965723..4045177 [GRCh37]
Chr17:1912473..3991926 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:193307-5652222)x1 copy number loss See cases [RCV000053384] Chr17:193307..5652222 [GRCh38]
Chr17:45835..5555542 [GRCh37]
Chr17:43098..5496266 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3-12(chr17:162016-12343901)x3 copy number gain See cases [RCV000138531] Chr17:162016..12343901 [GRCh38]
Chr17:45835..12247218 [GRCh37]
Chr17:11807..12187943 [NCBI36]
Chr17:17p13.3-12		 pathogenic
GRCh38/hg38 17p13.3(chr17:150732-3242868)x1 copy number loss See cases [RCV000142323] Chr17:150732..3242868 [GRCh38]
Chr17:525..3146162 [GRCh37]
Chr17:525..3092912 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:226472-3655099)x1 copy number loss See cases [RCV000135857] Chr17:226472..3655099 [GRCh38]
Chr17:396627..3558393 [GRCh37]
Chr17:76263..3505142 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3(chr17:1227482-2261786)x3 copy number gain See cases [RCV000136639] Chr17:1227482..2261786 [GRCh38]
Chr17:1130776..2165080 [GRCh37]
Chr17:1077526..2111830 [NCBI36]
Chr17:17p13.3		 likely pathogenic|uncertain significance
GRCh38/hg38 17p13.3(chr17:234496-2385512)x3 copy number gain See cases [RCV000052429] Chr17:234496..2385512 [GRCh38]
Chr17:396627..2288806 [GRCh37]
Chr17:84287..2235556 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:2012699-2644858)x1 copy number loss See cases [RCV000138311] Chr17:2012699..2644858 [GRCh38]
Chr17:1915993..2548152 [GRCh37]
Chr17:1862743..2494902 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:198748-7491129)x3 copy number gain See cases [RCV000134970] Chr17:198748..7491129 [GRCh38]
Chr17:50690..7394448 [GRCh37]
Chr17:48539..7335172 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3-12(chr17:165730-11404096)x3 copy number gain Chromosome 17p13.3 duplication syndrome [RCV003327726] Chr17:165730..11404096 [GRCh38]
Chr17:17p13.3-12		 pathogenic

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 326
Low 13 12 15 2 58 1 43 8 29 5 69 15 1 9 26 1
Below cutoff 667 709 563 153 407 87 1216 482 908 88 349 536 67 382 718

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000414776
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl172,232,680 - 2,233,610 (+)Ensembl
RefSeq Acc Id: NR_110888
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38172,232,678 - 2,233,610 (+)NCBI
T2T-CHM13v2.0172,119,929 - 2,120,861 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AL450226.1 COSMIC
Ensembl Genes ENSG00000225084 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000414776 ENTREZGENE
GTEx ENSG00000225084 GTEx
Human Proteome Map AL450226.1 Human Proteome Map
NCBI Gene LOC101927839 ENTREZGENE
RNAcentral URS000075C3BC RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AL450226.1  novel transcript, antisense to SMG6  LOC101927839  uncharacterized LOC101927839  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC101927839  uncharacterized LOC101927839  AL450226.1  novel transcript, antisense to SMG6  Symbol and/or name change 5135510 APPROVED