Gene detail

Detailed information of XP_068743510.1 in Montipora capricornis

Genomic Location: chr3:76043935...76048712
NR annotation: XP_029209450.2, collagen alpha-6(VI) chain-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068887409.1

CCAAAATTATGTGTAAAGCTCGAATTACACGGAAGTTTAATCGATTAGTTGACTGTGTGCGTTGGACGGGCTGATCGTGGACGGAAATTCGAAGATTATTTGATAAATATGTTGGCTTACGTATACGTAGGTCTCTTGAGCGTTGTTTTAACATTTCCAGTGTCTTTCAGCATCACTTGTAAACAATCTTACGATCCGAGCCGATACATTGGGAAAGCACGAGTGCCAGTGGATTGCAAGCCAGAACATTTGGGTTGTCCGAGCTCGTGGAAAGCGGGAGTACCAGAAATCGGCAGCGATCCCTCCAATGCCTTCGACGAAATGGTCGATACCAAATTTCTATACTGTCACGAAGGTTTTACGACGTGTGGTTATGTTCCCATTAATTCGAGAAATGGACAAGTTCTCGGCCACAGTGGCGTCACGATTGGAGCAGGAATTGATCTCGGAACAAAGACGAGCACTTCCTTCCAGGGCTTATCGGGTGATATCGTGAAAAAACTTGCACCATACTTCGGTTTGCAAAAAGATAAAGCAGCCTGTGCCATTATTCAAAATCCCTTACGACTTTCACGCGAGGAAGCCACGAAGACGACCAACGTGATAAAAATGCAGACACTAATCTCGGTTCAAAGCAGATACGATCAAGACAAGAAAGCAGGTGCAAAGAAATTCGATTCATTGCCACGTGGAATCCGCACGGCGATTGTCAGCGTTTGGTTTCAGTTTGGTTCACAACGAAACTATCCCAAGTTCTGGGGTCACGTCACGAAAAATGAATGGGAAAAGGCGGTGAATGAACTGAGAAATTTTTACAGCAATCCCAAAAGCCAAGCGCGCGGTGATTTGAGAAGACGGAACAACGAAGCGGACATAATCGAAGCAGCTGTTTCGAATTGCACAAGTTCAGTGGACCTTGTGTTTCTTCTTGACGAATCCGGAAGTGTTCGTGCCAATAACTTTCAAAAGAGCCTTGATTTCGTCCGACGCCTGATCGGATCATTTCCTGAAGAGAATTTACGTGGAGAAAATGGTACAAGGTTTGGTCTTTCAACTTTTTCCAGCAGCTACTCTACGAAATTCTACCTGTATAGTTATACAAATCAACTTGATTATTCCTCTGCAATAACAAGGGTCAGGTATTCCGGCGGAGGTACTCAACTTGGCTTTGCCCTTAGAAGGGTCTTAACAGATCAATTCTCGGAGCGGTTCGGTCTACGTCCGAAAGCCGACGGCTTGCCACGAATACTTGTCGTGCTGACAGATGGGGAATCGGGTGATAATGTTTCAACGCCGGCGAAAACAGTAAGAGATAATGAAATCACGATCTATGCAGTTGGAGTTGCCAGGTATAACTTAGAGCAACTTAAAGAGATCGCACCATCAGATCAACACGTCATCACCCTCGACTCGTTCTCAAAACTCGACGCTTTTGTTTCCACGATCACATCCTCGGCATGCTACGAGCCTCGGGCGTCGGGAAACAACGAAACCATCACGACGAACGTGAAAAAGGGCTCTTTTAAATATTTCAGCTACAAGGTGAATCCAGAAAAGAATCTCGAGGTAAGTGTGGACGATCTAGTTGGAAGTACCATGCTCTACGCATCTCGTACCACACCACATCCATATAAGTATGACCACGACTATAAGTTCGAGCGCGCGTCGCAGAAGGATAAAGTCATCGTGATAGGGGGAAATGCAACCTCCCCACGGCCGAAGCGATCGACTGGCAACAACCTTCAACCGATCTACATCGCCGTAACTTCAGACACCGACTCGGCGAAATTCACGATCGTGGCGAACGAGTGCGAGCCATCAGTATGCGTCGAAGGTACAAACGAGAGGAGGTCAGGATCGTCGAAGAATTACTCAAAATTTCCTTGGGTGTTCCTTCTCGGAAGCATTTCAGTGCTGTTGAATAACTATTACTAAATATACATCAATACAACTGTTTCGTGAAGAACAGTGCTTGCTTGACATTTGCGTGACGTTTAAAAGTTTATTTCGATTAGTATTACAATTTTTCCTTTCACTTATTGATTACATTGATTGACATTGAAATTTGAGCAATTTGATGGTTTTAGTTAGGTTTCTTTTACACGTGTCGTGTCGGCGGTATGGATCAGGATAGCTTTCccgtttttcaaggtttttacaATTTAGTTAAACTCTGGAATCCCGCCACGAAGTAAGTCATCAGTTGTTTATAATTTCCGTTTTCTTAGGCTTTGTCTTGGTCGATTGTTCCTTTTATTTCTGTCCGTGTATTTTTTGTAATTGACTGCATGTGATTAATAATTGTGCAATGCCGCATGGTTTTCTCAGTTAAATCTGTTCATGGTTTTAGGTTAATAAGTAAGTTAACAAGTCTTAACGAACAAACAGAAGAGGTTATTTCCTCTCCgctttatatttttttctccaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q21540	Cuticlin-6 OS=Caenorhabditis elegans OX=6239 GN=cut-6 PE=1 SV=2
P15989	Collagen alpha-3(VI) chain OS=Gallus gallus OX=9031 GN=COL6A3 PE=2 SV=2
P12111	Collagen alpha-3(VI) chain OS=Homo sapiens OX=9606 GN=COL6A3 PE=1 SV=5

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007506 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16754 all species →	Pesticin	Bacterial toxin homologue of phage lysozyme, C-term	Domain	Interproscan
PF00092 all species →	VWA	von Willebrand factor type A domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR023346 all species →	Homologous_superfamily	Lysozyme-like domain superfamily	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR031922 all species →	Domain	Pesticin, C-terminal	Interproscan
IPR050525 all species →	Family	Extracellular Matrix Assembly and Organization	Interproscan
IPR023347 all species →	Homologous_superfamily	Lysozyme domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24020 all species →	COLLAGEN ALPHA	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003796 all species →	Molecular Function	lysozyme activity	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

No KEGG orthology assignment for XP_068743510.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068743510.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples

28TPM > 0

1Conditions

896.1Max TPM

38.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	28	38.00	896.15

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	896.15
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	132.91
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	64.13
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	63.95
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	48.77
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	48.28
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	47.36
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	5.91
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	5.58
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	5.09
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	5.06
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	5.04
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	4.71
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	4.60
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	4.05
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	3.41
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	3.32
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	3.20
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	2.74
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	2.41
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	2.23
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	2.15
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	2.07
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	1.45
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	1.24
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	1.19
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	0.48
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	0.43
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	0.00
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.