Gene detail

Detailed information of g28480.t1 in Montipora capitata

Genomic Location: xfSc0000168:38923...56964
NR annotation: XP_044182513.1, laminin-like protein epi-1 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g28480.t1

atgaagaagggaagcttccttgaaagggttggggagactattttcggtgtgggtgaaacgaaggcctgccatgtagagcttgatggtcttgaagctaacctggtcggcgaggaacctggagcttgttactgtaaaaacaacaccatgggtaggcagtgcaacgagtgtaagccaggatatcacaatttatcagcagagaatcctgagggctgtcaagaatgcacctgttttcagcctggtacagtaaacggctcaaacatttgtgagcctgatgaacatggtgtttgtaattgtaagaagaatgttgaaggacaccgttgttccacttgtaagaacacctactttggtcttagtcaagaggatcttgatggctgcaaggagtgttcctgtgatgttggtggagcacttgggaatgtttgtaacaagacaactggtcagtgcaaatgcaaagaaagtatcacacagagacgttgtaacagtcctcaaaatggattttatttccccactctgcatttcatcagcagtgatttttcagaagtgattactagctctcagcagggaaacaagacatgggtcaccacagtcaacattgttcaaggagtgaattccagtggaatttttatgctgcttctttcctacacgagtacctccagtgttagaatcatgatcagcgtagagtcttttacagctgaagtgacccttagcaactgtacgcagctttgtttctccaacttgtcaacatttgcggaaatgtcactaactggttccgtggtggtcaatgttacgtccagagcatcagccagtcacttcaaaccagtgaaagttgtggcattaccacaagagttttaccaaccattgctactcggaaactcttctggtgatttcttggctaactgttttgtactagacaatgacattggtaaaggcactgatcatcacgagttttgcctggctcaagttttctcactcacagtaaactaccttggaggagctttatcatgcaactgtaatgagactggtgcagaaaacagcacgtgcctaaagtatggaggtcaatgccattgcaagcctggtgtaacaggaagaatgtgtgacaagtgtattgcaggattctataatttctcatcacaaggctgttcggcatgtggttgtgccagcgatgataaagtctgtgatgcagacactggacagtgtatttgtcctcccaataccattggtcgcacctgtaatcagtgtagtcacacgttctgggcatggaacgagacttttggatgccaggcctgcaactgcagtgacattggatccactgtttcacagtgtaacctcaccacaggagagtgtagctgtaatcctggtgtacagggagaaaagtgcatggaatgcatggatggttacaagaatttaacccgtcaaggctgttctctttgctcatgtaatgacaatggaagcttgagtgaagtgtgcaacaagtcctctggtcagtgcccttgtaagaacaactctgctggtttgctgtgtgatctgtgcaagagtggatttttttatctcatagacagtaatcccaaaggatgtacaaactgtgtttgtatgggaattactgcaaactgcagcagcacaacgctctacaggaaacagaaagaggttgatctggctttttggagtttagctttggctgatggaagccaaagctcatttgaagtttctgaagtctatatgatggatgaaagcatccgtgtaaaaatgattgctgcaaacatctcggctaatgacacagtgtattggaaagcaccagctaatttcacttatgagagtttggttggtgcatatggtggtaacttgagcttcaaagtttattttggagaattatacaatggaacactgcatatgtctaatccgaaaatcgtcttgaaaatgtactgggtttactcaaaagactcctcagcagtatccagggaagattttcttcttgtattggcaaaattgcaaactcttttgatcactgcctcattctattcagatggacaaggaacttaccttacaagccttggagatgcccacgttgctgaagtaggtgccatgccatctgatgatggaagagcttatgaagtggaaaagtgtaactgtggggttggttacgatggtttgtcttgtgagcgctgtgccagaggttatcacagagtcgatgtatcaagtgacaagtacctggggaaatgtcaggcatgcaactgtaatggacacacagaagactgcgaccctgtcactggacagtgtttgaattgtgtacacaacacgactggctttcattgtgagatctgtttggatggtttctacggcaatgcaactgatggaacaccaaacgactgcatggaatgcccatgtgaaaagccaagaacaaccactgcattgtgtgttggaggtctggatggtagacccaaatgcctaaattgttctgagggatatgagggcgacatttgtggaagtggagtttgtagtcatcgtgatgctccggccatggccacagttttagtcacaaatgaaacttaa

Transcript

g28480.t1

ATGAAGAAGGGAAGCTTCCTTGAAAGGGTTGGGGAGACTATTTTCGGTGTGGGTGAAACGAAGGCCTGCCATGTAGAGCTTGATGGTCTTGAAGCTAACCTGGTCGGCGAGGAACCTGGAGCTTGTTACTGTAAAAACAACACCATGGGTAGGCAGTGCAACGAGTGTAAGCCAGGATATCACAATTTATCAGCAGAGAATCCTGAGGGCTGTCAAGAATGCACCTGTTTTCAGCCTGGTACAGTAAACGGCTCAAACATTTGTGAGCCTGATGAACATGGTGTTTGTAATTGTAAGAAGAATGTTGAAGGACACCGTTGTTCCACTTGTAAGAACACCTACTTTGGTCTTAGTCAAGAGGATCTTGATGGCTGCAAGGAGTGTTCCTGTGATGTTGGTGGAGCACTTGGGAATGTTTGTAACAAGACAACTGGTCAGTGCAAATGCAAAGAAAGTATCACACAGAGACGTTGTAACAGtcctcAAAATGGATTTTATTTCCCCACTCTGCATTTCATCAGCAGTGATTTTTCAGAAGTGATTACTAGCTCTCAGCAGGGAAACAAGACATGGGTCACCACAGTCAACATTGTTCAAGGAGTGAATTCCAGTGGAATTTTTATGCTGCTTCTTTCCTACACGAGTACCTCCAGTGTTAGAATCATGATCAGCGTAGAGTCTTTTACAGCTGAAGTGACCCTTAGCAACTGTACGCAGCTTTGTTTCTCCAACTTGTCAACATTTGCGGAAATGTCACTAACTGGTTCCGTGGTGGTCAATGTTACGTCCAGAGCATCAGCCAGTCACTTCAAACCAGTGAAAGTTGTGGCATTACCACAAGAGTTTTACCAACCATTGCTACTCGGAAACTCTTCTGGTGATTTCTTGGCTAACTGTTTTGTACTAGACAATGACATTGGTAAAGGCACTGATCATCACGAGTTTTGCCTGGCTCAAGTTTTCTCACTCACAGTAAACTACCTTGGAGGAGCTTTATCATGCAACTGTAATGAGACTGGTGCAGAAAACAGCACGTGCCTAAAGTATGGAGGTCAATGCCATTGCAAGCCTGGTGTAACAGGAAGAATGTGTGACAAGTGTATTGCAGGATTCTATAATTTCTCATCACAAGGCTGTTCGGCATGTGGTTGTGCCAGCGATGATAAAGTCTGTGATGCAGACACTGGACAGTGTATTTGTCCTCCCAATACCATTGGTCGCACCTGTAATCAGTGTAGTCACACGTTCTGGGCATGGAACGAGACTTTTGGATGCCAGGCCTGCAACTGCAGTGACATTGGATCCACTGTTTCACAGTGTAACCTCACCACAGGAGAGTGTAGCTGTAATCCTGGTGTACAGGGAGAAAAGTGCATGGAATGCATGGATGGTTACAAGAATTTAACCCGTCAAGGCTGTTCTCTTTGCTCATGTAATGACAATGGAAGCTTGAGTGAAGTGTGCAACAAGTCCTCTGGTCAGTGCCCTTGTAAGAACAACTCTGCTGGTTTGCTGTGTGATCTGTGCAAGAGTGGATTTTTTTATCTCATAGACAGTAATCCCAAAGGATGTACAAActgtgtttgtatgggaattacTGCAAACTGCAGCAGCACAACGCTCTACAGGAAACAGAAAGAGGTTGATCTGGCTTTTTGGAGTTTAGCTTTGGCTGATGGAAGCCAAAGCTCATTTGAAGTTTCTGAAGTCTATATGATGGATGAAAGCATCCGTGTAAAAATGATTGCTGCAAACATCTCGGCTAATGACACAGTGTATTGGAAAGCACCAGCTAATTTCACTTATGAGAGTTTGGTTGGTGCATATGGTGGTAACTTGAGCttcaaagtttattttggaGAATTATACAATGGAACACTGCATATGTCTAATCCGAAAATCGTCTTGAAAATGTACTGGGTTTACTCAAAAGACTCCTCAGCAGTATCCAGGGAAGATTTTCTTCTTGTATTGGCAAAATTGCAAACTCTTTTGATCACTGCCTCATTCTATTCAGATGGACAAGGAACTTACCTTACAAGccttgGAGATGCCCACGTTGCTGAAGTAGGTGCCATGCCATCTGATGATGGAAGAGCTTATGAAGTGGAAAAGTGTAACTGTGGGGTTGGTTACGATGGTTTGTCTTGTGAGCGCTGTGCCAGAGGTTATCACAGAGTCGATGTATCAAGTGACAAGTACCTGGGGAAATGTCAGGCATGCAACTGTAATGGACACACAGAAGACTGCGACCCTGTCACTGGACAGTGTTTGAATTGTGTACACAACACGACTGGCTTTCATTGTGAGATCTGTTTGGATGGTTTCTACGGCAATGCAACTGATGGAACACCAAACGACTGCATGGAATGCCCATGTGAAAAGCCAAGAACAACCACTGCATTGTGTGTTGGAGGTCTGGATGGTAGACCCAAATGCCTAAATTGTTCTGAGGGATATGAGGGCGACATTTGTGGAAGTGGAGTTTGTAGTCATCGTGATGCTCCGGCCATGGCCACAGTTTTAGTCACAAATGAAACTTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q21313	Laminin-like protein epi-1 OS=Caenorhabditis elegans OX=6239 GN=epi-1 PE=1 SV=1
Q05793	Basement membrane-specific heparan sulfate proteoglycan core protein OS=Mus musculus OX=10090 GN=Hspg2 PE=1 SV=1
P98160	Basement membrane-specific heparan sulfate proteoglycan core protein OS=Homo sapiens OX=9606 GN=HSPG2 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001117 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00053 all species →	Laminin_EGF	Laminin EGF domain	Domain	Interproscan
PF00052 all species →	Laminin_B	Laminin B (Domain IV)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002049 all species →	Domain	Laminin-type EGF domain	Interproscan
IPR050440 all species →	Family	Laminin/Netrin Extracellular Matrix	Interproscan
IPR000034 all species →	Domain	Laminin IV	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10574 all species →	NETRIN/LAMININ-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0009887 all species →	Biological Process	animal organ morphogenesis	Interproscan
GO:0009888 all species →	Biological Process	tissue development	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0034446 all species →	Biological Process	substrate adhesion-dependent cell spreading	Interproscan
GO:0043256 all species →	Cellular Component	laminin complex	Interproscan
GO:0070831 all species →	Biological Process	basement membrane assembly	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 g28480.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g28480.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

39TPM > 0

3Conditions

15.3Max TPM

3.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	18	3.79	14.66
whole organisms · low pH treatment	15	11	2.70	9.40
whole organisms · extra low pH treatment pH treatment	12	10	4.68	15.30

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	14.66
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	12.28
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	10.94
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	8.49
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	6.69
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	5.69
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	4.12
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	3.15
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	2.10
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	2.08
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	1.92
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	1.81
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	1.55
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	1.10
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	1.07
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	0.71
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	0.70
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.45
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.00
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	0.00
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	0.00
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	9.40
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	8.72
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	7.35
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	3.81
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	2.73
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	2.53
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	1.67
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	1.57
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	1.38
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.82
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	0.47
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	0.00
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.00
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	15.30
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	13.67
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	10.40
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	7.19
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	3.71
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	2.54
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	1.48
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	1.23
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	0.37
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	0.31
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.