Gene detail

Detailed information of g7014.t1 in Acropora digitifera

Genomic Location: chr3Alt:25761827...25778941
NR annotation: XP_029190659.2, very low-density lipoprotein receptor-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g7014.t1

ATGACTCTTTTGGCTAAGGCTGTTGTGTTGTGCGTTGTACACTCTGTTGTTGTGGCTACTTCCTCTTCTAATGCATCTTTCCATTGTGGAGATGGCAAGTTTGCCTGTGGAAGTCAGAAGTGTATACCTGATCGTTGGAGGTGTGATGACTATGATGACTGTGGAGATCAATCAGATGAAGTCGGATGCCCTGAGAAGACTTGTTTGGATCATCGCTTCAATTGTACCAATGGACGCTGTGTCTGGAAATCATTTGTGTGTGACTTTGATGATGATTGTGGAGATGGATCGGATGAAGTTGGTTGTGATCGTAACCACACCTGTCCTGATAACAAGTTTAAATGTAAAAGTGGAAAATGCATTGATATCTTGTGGAAGTGCGATGGAGAAAATGATTGTGTGGATAATTCAGATGAAACCAGTTGTGAAACAGCAACATGCCCATCCAACAAGTTTACTTGTAATAACAACAATTGTGTACCACGCTCCCATCTTTGTGATGGAGATGACGATTGTGAAGATAATTCAGATGAAACAACTGACCAATGTGCAAGTTTGACTTGCAGCAGCAACCAATTTACTTGTCCCAATCACATGTGTATTCCAAGCCGCTGGAGATGCGATGGCGATGCAGACTGTTCAGATGGCTCTGATGAGAAAGGCTGTAATACACACATTACACGTTCTCCTCAAGTTTGCGCAGAACAAATGTTCAGTTGTAATGACGGAAATTGCATCAGAAACAGTTGGCGCTGCGATGGGGAAAATGATTGCCAAGATGGATCTGATGAAGAAAGATGTTCAACATGTTCATCTGACAAATTCAAGTGTGGCAACGCCTCTCTGTGTATTCCACAAAGCCAAAGATGCAATGGTAAGAGAGACTGTCCAAATGGAGAGGATGAGCCACTGAGTTGCGAAATTAATGAATGTGCGTATTTCAATGGTCATTGTCAACAAGTTTGCACAGATCTTAAAGTTGGCTTTGAATGTTCGTGTCATCCTGGGTTCAAACTTGCTAATGACCAGAAAACATGTGAAGATATTGATGAATGTGAGGTGTTTGGACAATGTAGTCAAGACTGCATCAACATGAAGGGAACGTTCGAATGTTCCTGTAAACCTGGCTACCACTTGGATGCCAACAAAATGCTTTGCAGAGCAGCTGAGACTACACCATATTTGATGTTCTCAACACAGCGCACTATTCGCAAACTTGCAATTGGGAGATTGTTTCATGACTACAGCGATGTTGTCAGAAGTCAGAAAGGAATTGCAGCACTGGACTATGACTATCGTGAAAATTATTTGTTCTGGACAGATATAAGAGATGAAAGGATTTGTGGTGCTCGCATTCCAAGCCAAGATACCACGGCAGCTCTTTGTGAGCGGACAGTAGTTTCAAGTGTCAGTTCTCCTGAAGGCATTGCTGTTGACTGGGCTACAAAGAAAATATATTGGACTGATGGAGGCCACAATGTGATTGAGGTTGCTGAATTTGATGGCTCACACAGACTCACCTTGTTTTATAATGACATATATGATCCAAGAGCCATAGTGGTCGATCCTTTTCATGGGTATCTGTTTTGGACAGACTGGTTCACTAACAGCCCAAGAATCGAAAGATCAGGGATGGACGGAAATCCATCGACAAGAACAGTGGTTGTATCTGAGCGCTTGGGTTGGCCAAATGCACTGGCTATTGATTATACTTTGCAACGAATTTTCTGGGCTGATGCGAAACTCAAGACGGTAGAATCAAGCACCTATGATGGCACTGATCGCCGTGTGATTGCCGTCATTACGCCACATCACCCTTACAGTATGGATTTGTTTGAGAATCATCTGTACTACACAGACTGGTATAGATTTGACAGAGGGATCAGGAGCATGAACAAATTCAATGGAAGTGATGAACACAAGATCTCGTCTGTTCGATTTTGGACAAACATGGGCATTCGAGTATACCACCCCCTTCGTCAGCCAAACGTCACCAACCCATGTGAGGTGAATAATGGTAATTGCAGCCATCTTTGTCTGTTGGCTGTTGCCCCAATGGGGCGCTCGTGCCGCTGCCCTAATGGTATGGAAATGTCATCCGGTAATGGCACCTGCACAGGAACACCAATCAACAGACCTGTTGGACCAAATAGACCAGCAACGACCCCATCTTCCCAATCGACTACAAAGGCTTCCACGGCTGAACCTACGACCCCAACGAGTAAACCTTTGGATTCTGTGACAACATCTAGTCCATCCAAAGCACCAGGTTCAAAAACTGAACAGGGAAAAGATGAATCCAAGACCGTCAGTACAGCATCTCCAACCAAACCTAGTACTAAACCCTCACGAGCCAGGTCCAATGAATCTCTTAGGAAGACTACTTCACCAACAGCCTCTGGAAAAACTGCGACAAAGGAAGATTCAAACTCAACCCAGAAGCTTGAGGATCCAATTATTGTATCAGCCAAAAGAAAAGATAACAGCAAACATCGGGGTCTTCCTAGCGGTGCTATAATTGGCATAGTCGTTGCTATAGTTTTCGTCGTTGTGTTTGTTGTTGGGACAATATGGTTTATGCTGCGTCGCACTAAATCCTATGGCGGGAAGACTATCGTGTACCACAAAGATGCAACCACAAAACCACTGGCAGAAGATTTTGATAACGATGAATCGTTCAAGGCATTTGATGACAAGGCATACCGTGAAAGGGTTGAATTTGCGTAA

Transcript

chr3Alt.g7014.t1

ACATTCAAAATAAGAAGAAGTTGTCACAGAAAGTTTCTTCTTCTGGTTCTTCTTTTGGACGAAACATGACTCTTTTGGCTAAGGCTGTTGTGTTGTGCGTTGTACACTCTGTTGTTGTGGCTACTTCCTCTTCTAATGCATCTTTCCATTGTGGAGATGGCAAGTTTGCCTGTGGAAGTCAGAAGTGTATACCTGATCGTTGGAGGTGTGATGACTATGATGACTGTGGAGATCAATCAGATGAAGTCGGATGCCCTGAGAAGACTTGTTTGGATCATCGCTTCAATTGTACCAATGGACGCTGTGTCTGGAAATCATTTGTGTGTGACTTTGATGATGATTGTGGAGATGGATCGGATGAAGTTGGTTGTGATCGTAACCACACCTGTCCTGATAACAAGTTTAAATGTAAAAGTGGAAAATGCATTGATATCTTGTGGAAGTGCGATGGAGAAAATGATTGTGTGGATAATTCAGATGAAACCAGTTGTGAAACAGCAACATGCCCATCCAACAAGTTTACTTGTAATAACAACAATTGTGTACCACGCTCCCATCTTTGTGATGGAGATGACGATTGTGAAGATAATTCAGATGAAACAACTGACCAATGTGCAAGTTTGACTTGCAGCAGCAACCAATTTACTTGTCCCAATCACATGTGTATTCCAAGCCGCTGGAGATGCGATGGCGATGCAGACTGTTCAGATGGCTCTGATGAGAAAGGCTGTAATACACACATTACACGTTCTCCTCAAGTTTGCGCAGAACAAATGTTCAGTTGTAATGACGGAAATTGCATCAGAAACAGTTGGCGCTGCGATGGGGAAAATGATTGCCAAGATGGATCTGATGAAGAAAGATGTTCAACATGTTCATCTGACAAATTCAAGTGTGGCAACGCCTCTCTGTGTATTCCACAAAGCCAAAGATGCAATGGTAAGAGAGACTGTCCAAATGGAGAGGATGAGCCACTGAGTTGCGAAATTAATGAATGTGCGTATTTCAATGGTCATTGTCAACAAGTTTGCACAGATCTTAAAGTTGGCTTTGAATGTTCGTGTCATCCTGGGTTCAAACTTGCTAATGACCAGAAAACATGTGAAGATATTGATGAATGTGAGGTGTTTGGACAATGTAGTCAAGACTGCATCAACATGAAGGGAACGTTCGAATGTTCCTGTAAACCTGGCTACCACTTGGATGCCAACAAAATGCTTTGCAGAGCAGCTGAGACTACACCATATTTGATGTTCTCAACACAGCGCACTATTCGCAAACTTGCAATTGGGAGATTGTTTCATGACTACAGCGATGTTGTCAGAAGTCAGAAAGGAATTGCAGCACTGGACTATGACTATCGTGAAAATTATTTGTTCTGGACAGATATAAGAGATGAAAGGATTTGTGGTGCTCGCATTCCAAGCCAAGATACCACGGCAGCTCTTTGTGAGCGGACAGTAGTTTCAAGTGTCAGTTCTCCTGAAGGCATTGCTGTTGACTGGGCTACAAAGAAAATATATTGGACTGATGGAGGCCACAATGTGATTGAGGTTGCTGAATTTGATGGCTCACACAGACTCACCTTGTTTTATAATGACATATATGATCCAAGAGCCATAGTGGTCGATCCTTTTCATGGGTATCTGTTTTGGACAGACTGGTTCACTAACAGCCCAAGAATCGAAAGATCAGGGATGGACGGAAATCCATCGACAAGAACAGTGGTTGTATCTGAGCGCTTGGGTTGGCCAAATGCACTGGCTATTGATTATACTTTGCAACGAATTTTCTGGGCTGATGCGAAACTCAAGACGGTAGAATCAAGCACCTATGATGGCACTGATCGCCGTGTGATTGCCGTCATTACGCCACATCACCCTTACAGTATGGATTTGTTTGAGAATCATCTGTACTACACAGACTGGTATAGATTTGACAGAGGGATCAGGAGCATGAACAAATTCAATGGAAGTGATGAACACAAGATCTCGTCTGTTCGATTTTGGACAAACATGGGCATTCGAGTATACCACCCCCTTCGTCAGCCAAACGTCACCAACCCATGTGAGGTGAATAATGGTAATTGCAGCCATCTTTGTCTGTTGGCTGTTGCCCCAATGGGGCGCTCGTGCCGCTGCCCTAATGGTATGGAAATGTCATCCGGTAATGGCACCTGCACAGGAACACCAATCAACAGACCTGTTGGACCAAATAGACCAGCAACGACCCCATCTTCCCAATCGACTACAAAGGCTTCCACGGCTGAACCTACGACCCCAACGAGTAAACCTTTGGATTCTGTGACAACATCTAGTCCATCCAAAGCACCAGGTTCAAAAACTGAACAGGGAAAAGATGAATCCAAGACCGTCAGTACAGCATCTCCAACCAAACCTAGTACTAAACCCTCACGAGCCAGGTCCAATGAATCTCTTAGGAAGACTACTTCACCAACAGCCTCTGGAAAAACTGCGACAAAGGAAGATTCAAACTCAACCCAGAAGCTTGAGGATCCAATTATTGTATCAGCCAAAAGAAAAGATAACAGCAAACATCGGGGTCTTCCTAGCGGTGCTATAATTGGCATAGTCGTTGCTATAGTTTTCGTCGTTGTGTTTGTTGTTGGGACAATATGGTTTATGCTGCGTCGCACTAAATCCTATGGCGGGAAGACTATCGTGTACCACAAAGATGCAACCACAAAACCACTGGCAGAAGATTTTGATAACGATGAATCGTTCAAGGCATTTGATGACAAGGCATACCGTGAAAGGGTTGAATTTGCGTAAGAAAATCTGTTTGAACTGTCTATTATTAGTAGTATCTGGTTAACTTGAGAAAGATGCGATAGGGCAACTCTTTCTCCCAACGAAAAAGGCAACAGCATCTAAAATTCAGCGCCCAGCCATAAACAATCTTGACCATT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
C0HL13	Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1
Q04833	Low-density lipoprotein receptor-related protein OS=Caenorhabditis elegans OX=6239 GN=lrp-1 PE=1 SV=1
A2ARV4	Low-density lipoprotein receptor-related protein 2 OS=Mus musculus OX=10090 GN=Lrp2 PE=1 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00057 all species →	Ldl_recept_a	Low-density lipoprotein receptor domain class A	Repeat	Interproscan
PF12662 all species →	cEGF	Complement Clr-like EGF-like	Domain	Interproscan
PF00058 all species →	Ldl_recept_b	Low-density lipoprotein receptor repeat class B	Repeat	Interproscan
PF14670 all species →	FXa_inhibition	Coagulation Factor Xa inhibitory site	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002172 all species →	Repeat	Low-density lipoprotein (LDL) receptor class A repeat	Interproscan
IPR000033 all species →	Repeat	LDLR class B repeat	Interproscan
IPR036055 all species →	Homologous_superfamily	LDL receptor-like superfamily	Interproscan
IPR026823 all species →	Domain	Complement Clr-like EGF domain	Interproscan
IPR023415 all species →	Conserved_site	Low-density lipoprotein (LDL) receptor class A, conserved site	Interproscan
IPR000152 all species →	PTM	EGF-type aspartate/asparagine hydroxylation site	Interproscan
IPR001881 all species →	Domain	EGF-like calcium-binding domain	Interproscan
IPR051221 all species →	Family	Low-density lipoprotein receptor-related	Interproscan
IPR018097 all species →	Conserved_site	EGF-like calcium-binding, conserved site	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR009030 all species →	Homologous_superfamily	Growth factor receptor cysteine-rich domain superfamily	Interproscan
IPR011042 all species →	Homologous_superfamily	Six-bladed beta-propeller, TolB-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22722 all species →	LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006898 all species →	Biological Process	receptor-mediated endocytosis	Interproscan
GO:0016324 all species →	Cellular Component	apical plasma membrane	Interproscan
GO:0042562 all species →	Molecular Function	hormone binding	Interproscan
GO:0043235 all species →	Cellular Component	receptor complex	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K20053	VLDLR; very low-density lipoprotein receptor	-	Membrane trafficking	ko04131	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of g7014.t1 across 39 RNA-seq samples of Acropora digitifera. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

39Samples

39TPM > 0

1Conditions

97.3Max TPM

42.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	42.72	97.27

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	97.27
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	75.96
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	68.10
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	63.96
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	62.54
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	53.72
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	51.30
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	47.72
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	46.83
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	46.33
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	44.74
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	44.27
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	43.62
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	43.44
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	40.86
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	40.30
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	40.21
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	40.16
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	39.07
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	38.84
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	38.80
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	38.55
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	38.01
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	36.81
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	35.46
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	35.45
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	35.19
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	35.11
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	34.31
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	33.60
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	32.55
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	32.08
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	31.98
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	31.92
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	31.44
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	31.09
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	29.16
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	28.13
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	27.25

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Acropora digitifera tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	12	g8643.t1	0.81006890603821
Negatively correlated	7	g4777.t1	-0.632079884193115

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora digitifera, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

Peak calls overlapping this gene

Assay	Sample	Peaks	Region
DNase-seq (DHS)	WholeAnimal	2	Distal Intergenic 2

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →