AL590226.1 (novel transcript, antisense to EGFL7 (HSPC324)) - Rat Genome Database

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Gene: AL590226.1 (novel transcript, antisense to EGFL7 (HSPC324)) Homo sapiens
Analyze
Symbol: AL590226.1
Name: novel transcript, antisense to EGFL7 (HSPC324)
RGD ID: 16554094
Description: INTERACTS WITH benzo[a]pyrene
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: HSPC324; uncharacterized LOC101928612
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,648,610 - 136,660,421 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,647,872 - 136,660,421 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,648,610 - 136,660,421 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,543,062 - 139,554,873 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map9q34.3NCBI
HuRef9109,003,237 - 109,015,058 (-)NCBIHuRef
CHM1_19139,691,362 - 139,703,206 (-)NCBICHM1_1
T2T-CHM13v2.09148,881,592 - 148,893,402 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:32068121  


Genomics

Variants

.
Variants in AL590226.1
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9q34.3(chr9:136323974-138014606)x1 copy number loss See cases [RCV000148284] Chr9:136323974..138014606 [GRCh38]
Chr9:139218428..140909058 [GRCh37]
Chr9:138338249..140028879 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134174698-138138735)x3 copy number gain See cases [RCV000053814] Chr9:134174698..138138735 [GRCh38]
Chr9:137091194..141033187 [GRCh37]
Chr9:136029641..140153008 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:122792658-138124532)x3 copy number gain See cases [RCV000051040] Chr9:122792658..138124532 [GRCh38]
Chr9:125554937..141018984 [GRCh37]
Chr9:124594758..140138805 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:130513207-138124532)x3 copy number gain See cases [RCV000133778] Chr9:130513207..138124532 [GRCh38]
Chr9:133388594..141018984 [GRCh37]
Chr9:132378415..140138805 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:129068560-138179445)x3 copy number gain See cases [RCV000134916] Chr9:129068560..138179445 [GRCh38]
Chr9:131830839..141073897 [GRCh37]
Chr9:130870660..140193718 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3 copy number gain See cases [RCV000136790] Chr9:132986903..138114463 [GRCh38]
Chr9:135862290..141008915 [GRCh37]
Chr9:134852111..140128736 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132386553-138059695)x3 copy number gain See cases [RCV000142636] Chr9:132386553..138059695 [GRCh38]
Chr9:135261940..140954147 [GRCh37]
Chr9:134251761..140073968 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135704780-138125937)x4 copy number gain See cases [RCV000143394] Chr9:135704780..138125937 [GRCh38]
Chr9:138596626..141020389 [GRCh37]
Chr9:137736447..140140210 [NCBI36]
Chr9:9q34.3		 likely pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121112395-138075224)x3 copy number gain See cases [RCV000051009] Chr9:121112395..138075224 [GRCh38]
Chr9:123874673..140969676 [GRCh37]
Chr9:122914494..140089497 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121073102-138179445)x3 copy number gain See cases [RCV000134920] Chr9:121073102..138179445 [GRCh38]
Chr9:123835380..141073897 [GRCh37]
Chr9:122875201..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133996227-138124524)x3 copy number gain See cases [RCV000139807] Chr9:133996227..138124524 [GRCh38]
Chr9:136861349..141018976 [GRCh37]
Chr9:135851170..140138797 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135452016-137613738)x1 copy number loss See cases [RCV000052937] Chr9:135452016..137613738 [GRCh38]
Chr9:138343862..140508190 [GRCh37]
Chr9:137483683..139628011 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:136323974-138014606)x1 copy number loss See cases [RCV000050344] Chr9:136323974..138014606 [GRCh38]
Chr9:139218428..140909058 [GRCh37]
Chr9:138338249..140028879 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:136323974-138124532)x1 copy number loss See cases [RCV000051116] Chr9:136323974..138124532 [GRCh38]
Chr9:139218428..141018984 [GRCh37]
Chr9:138338249..140138805 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134428674-138154922)x1 copy number loss See cases [RCV000052936] Chr9:134428674..138154922 [GRCh38]
Chr9:137320520..141049374 [GRCh37]
Chr9:136460341..140169195 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133504071-138159073)x3 copy number gain See cases [RCV000137825] Chr9:133504071..138159073 [GRCh38]
Chr9:136324358..141053525 [GRCh37]
Chr9:135314179..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133918071-138159073)x3 copy number gain See cases [RCV000142955] Chr9:133918071..138159073 [GRCh38]
Chr9:136783193..141053525 [GRCh37]
Chr9:135773014..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:134962336-137240181)x1 copy number loss See cases [RCV002640756] Chr9:134962336..137240181 [GRCh38]
Chr9:9q34.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:556
Count of miRNA genes:449
Interacting mature miRNAs:492
Transcripts:ENST00000408766, ENST00000411904, ENST00000597530
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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2 5 30 25 113 1 3 2 408 123 2
Low 1919 1968 1391 423 520 285 3256 1707 1545 316 1004 935 137 1 1079 2207 1 2
Below cutoff 381 473 249 168 368 143 666 425 1809 55 318 89 33 2 517 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000411904
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,648,610 - 136,649,132 (-)Ensembl
RefSeq Acc Id: ENST00000674687
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,647,872 - 136,660,457 (-)Ensembl
RefSeq Acc Id: ENST00000675837
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,648,610 - 136,660,414 (-)Ensembl
RefSeq Acc Id: ENST00000686327
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,648,619 - 136,660,403 (-)Ensembl
RefSeq Acc Id: ENST00000687828
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,648,610 - 136,660,420 (-)Ensembl
RefSeq Acc Id: ENST00000691577
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,648,614 - 136,660,414 (-)Ensembl
RefSeq Acc Id: ENST00000692865
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,647,872 - 136,660,457 (-)Ensembl
RefSeq Acc Id: ENST00000700885
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,648,619 - 136,660,431 (-)Ensembl
RefSeq Acc Id: ENST00000701344
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,648,614 - 136,660,387 (-)Ensembl
RefSeq Acc Id: NR_135132
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389136,648,610 - 136,660,421 (-)NCBI
T2T-CHM13v2.09148,881,592 - 148,893,402 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein AAF29002 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC AL590226.1 COSMIC
Ensembl Genes ENSG00000228401 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000675837 ENTREZGENE
GTEx ENSG00000228401 GTEx
Human Proteome Map AL590226.1 Human Proteome Map
NCBI Gene HSPC324 ENTREZGENE
RNAcentral URS0000A76720 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-08-20 AL590226.1  novel transcript, antisense to EGFL7 (HSPC324)  AL590226.1  novel transcript  Symbol and/or name change 19259462 PROVISIONAL
2020-06-25 AL590226.1  novel transcript  HSPC324  uncharacterized LOC101928612  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 HSPC324  uncharacterized LOC101928612  AL590226.1  novel transcript  Symbol and/or name change 5135510 APPROVED