Gene detail

Detailed information of g7212.t1 in Montipora capitata

Genomic Location: Sc0000162:235996...248265
NR annotation: XP_029211951.2, uncharacterized protein LOC114975854 isoform X2 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g7212.t1

atgccgattcaaacaccacagtggacagagtttcttcaatgtccgatatgtaccaatgactttgatgacctcagccgacaaccaatcagcttgggatgtggtcatactatgtgtgtttcttgtttatcaaagctgccgaaaacacagtgtccatttgaccaggctatagttgaaactgatatctcagagcttccttataactatgctctccttcagttagttggagtccaaatcccagataaggcgcctcctaacataggaagcattcggaacaatgcttctcagtatcaagctgccaaacgttctattgaagaccttgcaatgtttttgcaaccagtagctggttctagcaatggaattgttaatggtactggcaatggaaatacctgtaatggtggtctcaatggaaatggcaatagtctgcttacaaggcctatgcaacgtaagctggttaccttagtaaactgtcaactggcggaagctgatggacgaatcagggctatgcgtgctgctcggagccttggggaaaggactgttactgagcttattttattgcaccaaaatcaacaacaactgtctggaaatttgtgggctgctgtgcgcaatcgtggttgtcaatttttaggaccagcaatgcaggaggaggcattgaaacttattttgttggcacttgaggggggtgaagcactgtctaggaaagttttggttctgtttgtggtccagaagcttgaatcacaatttccacaagcttcaaaaacaagcattggccatgtagtgcagttactttacagggcatcctgttttaaggtggaaaaaaagaacaatgaatcatctttgatgcagcttaaagaacagtttcgcacttacgatgcactgagaaaggagcatgatgcacagattgttcaaattgcaactgaagcaggactgcgtattctccctgatcagtggtcctcacttctctacggagatcttgatcacaagtcgcacatgcagtctattattgacaagctgcaatctcctgaatcattttctcaaagcattcaggagttggtgattgcacttcagaggtctggcgaccctggtgatttgtgccaaatgaaggaacagtttgaatttctctctcagattgatgcgtcaccagaggcaacatgtcctgagtggaaagaactagagaaggctatgaaagcagtgcattcagtcgttcatgggctggtgaagttttcaaaagcttatggcaagggaatgaggggctcaagtgacccaccccagcctcacaatggcaacaaatttaaaacaaacatgtgtagggatcattcacgaggtggatgtccacggggaattcactgcacctttgcacactctgaggaggaactagagaggtttagcaaaagacggcaacgggcacctcgccctacagctattcccagaggaccaggacctgttgcaggtccagatcaatattcacctcatggctccatagaaaatggctgtgaaaatagcccaacggccacgcaggctcctacaagtgctgttaatggatcagcgaggtcttcaccacattattcttcaggtgaaatgtcacacttttcatctggttatggggccccacctcaggttagtcgtagggacagccaggaacaaatccagatgattacacagagaatgaagcaagtctccatacagtcacaacagcccatgtaccagaatgatgcatactgtggatcgcgtttgcaatacgatcatgtgccgttaccgtatgcaccatcttcaggaagtgacagggcaacatattttcagggatactattctccatcagctacaccacatggcaattcatattctaatgttgtgtctcgaggaaaggacggaacagtaggaattatgaccccaccttgcaactcacccttgacgattcaggatgaagcaatgaccaaaatgaatggactcagtgggatgaacggactgaatgggatgaatggattgaatggaatgaatgggttaaatggaatgacaaatggacacgtggatcaccatcactctatgtacaatggcagggcggtgcgtccaagaagagatatggcacccttacaatcacagccaccaggaactagtggctatccacgttatgatcaatcatcatttggctatccatcagatcccactggttattgcagtgctcaacctgattactatagtcttgcatatgggagggctgccgtgtcttatgaacctgtcccacagactatcatgggctactctttcacaagacaataccacgatcctcgctttggatcaagaaagccatacattccaggcaatgatccatttgaagaacctggaaatgaaaacaatgatacagcaactgaatatgagcccatccttagttttggagttcttaacaggaaggacacgacactgtctagtgccagcagtggggtcagcagtggctccccactcagccactctcctgctgctagccaatcgtcaaactccagtttatcaccgaggcaacagtcccctgtggggtggcaacatgggagcgagaatgacttcagcaacgtgaaccttaaattcttagaggacagtagtactctgccaccgcccccgggtatcaacaatactgcaccaatatggtcacctcattgtggcaacgagaggggcaagctgtggacccgctatagtgtagacttcgacgagtggtcgaggaaagaggagcagataaaaaacgatgagcagtttgcgcgagctcttcaggagaaactccaacatgacagcaaatcgtcggaaataatcggcagtgaattgttaggatcgcgggacaacaaagaccaaggcattgatcaggggaggagagggcagaacgttccagattgcggcataggaatggacagcttggagactgaagcagaaatcaagaaacgaaagaaggaagaacacaggcgtctacttcaggaacgtagaaatctgcttcagcaacaggaaagagaaaaacaggagcgagatgatcgtatacttgccgaggaactagccttaaatgatgctcaacaagcagggctcttccctgatcctaggtgcatcgtgaaaccctattccagtgtgatttcccgcggggcccccatggggatcggtttcggcagccagggaagcagtgatgtttcaggggagttagatacgtttagcggttttggcagctttcgtggatcatgtgcatcttcattggctaataatgacgaaggcatagattcatcacagatgacgtcaggttgcagtggagacatacgtgtgcaagagtga

Transcript

g7212.t1

ATGCCGATTCAAACACCACAGTGGACAGAGTTTCTTCAATGTCCGATATGTACCAATGACTTTGATGACCTCAGCCGACAACCAATCAGCTTGGGATGTGGTCATACTATGTGTGTTTCTTGTTTATCAAAGCTGCCGAAAACACAGTGTCCATTTGACCAGGCTATAGTTGAAACTGATATCTCAGAGCTTCCTTATAACTATGCTCTCCTTCAGTTAGTTGGAGTCCAAATCCCAGATAAGGCGCCTCCTAACATAGGAAGCATTCGGAACAATGCTTCTCAGTATCAAGCTGCCAAACGTTCTATTGAAGACCTTGCAATGTTTTTGCAACCAGTAGCTGGTTCTAGCAATGGAATTGTTAATGGTACTGGCAATGGAAATACCTGTAATGGTGGTCTCAATGGAAATGGCAATAGTCTGCTTACAAGGCCTATGCAACGTAAGCTGGTTACCTTAGTAAACTGTCAACTGGCGGAAGCTGATGGACGAATCAGGGCTATGCGTGCTGCTCGGAGCCTTGGGGAAAGGACTGTTACTGAGCTTATTTTATTGCACCAAAATCAACAACAACTGTCTGGAAATTTGTGGGCTGCTGTGCGCAATCGTGGTTGTCAATTTTTAGGACCAGCAATGCAGGAGGAGGCATTGAAACTTATTTTGTTGGCACTTGAGGGGGGTGAAGCACTGTCTAGGAAAGTTTTGGTTCTGTTTGTGGTCCAGAAGCTTGAATCACAATTTCCACAAGCTTCAAAAACAAGCATTGGCCATGTAGTGCAGTTACTTTACAGGGCATCCTGTTTTAAGgtggaaaaaaagaacaatgaaTCATCTTTGATGCAGCTTAAAGAACAGTTTCGCACTTACGATGCACTGAGAAAGGAGCATGATGCACAGATTGTTCAAATTGCAACTGAAGCAGGACTGCGTATTCTCCCTGATCAGTGGTCCTCACTTCTCTACGGAGATCTTGATCACAAGTCGCACATGCAGTCTATTATTGACAAGCTGCAATCTCCTGAATCATTTTCTCAAAGCATTCAGGAGTTGGTGATTGCACTTCAGAGGTCTGGCGACCCTGGTGATTTGTGCCAAATGAAGGAACAGTTTGAATTTCTCTCTCAGATTGATGCGTCACCAGAGGCAACATGTCCTGAGTGGAAAGAACTAGAGAAGGCTATGAAAGCAGTGCATTCAGTCGTTCATGGGCTGGTGAAGTTTTCAAAAGCTTATGGCAAGGGAATGAGGGGCTCAAGTGACCCACCCCagCCTCACAATGGcaacaaatttaaaacaaacatGTGTAGGGATCATTCACGAGGTGGATGTCCACGGGGAATTCACTGCACCTTTGCACACTCTGAGGAGGAACTAGAGAGGTTTAGCAAAAGACGGCAACGGGCACCTCGCCCTACAGCTATTCCCAGAGGACCAGGACCTGTTGCAGGTCCAGATCAATATTCACCTCATGGCTCCATAGAAAATGGCTGTGAAAATAGCCCAACGGCCACGCAGGCTCCTACAAGTGCTGTTAATGGATCAGCGAGGTCTTCACCACATTATTCTTCAGGTGAAATGTCACACTTTTCATCTGGTTATGGGGCCCCACCTCAGGTTAGTCGTAGGGACAGCCAGGAACAAATCCAGATGATTACACAGAGAATGAAGCAAGTCTCCATACAGTCACAACAGCCCATGTACCAGAATGATGCATACTGTGGATCGCGTTTGCAATACGATCATGTGCCGTTACCGTATGCACCATCTTCAGGAAGTGACAGGGCAACATATTTTCAGGGATACTATTCTCCATCAGCTACACCACATGGCAATTCATATTCTAATGTTGTGTCTCGAGGAAAGGACGGAACAGTAGGAATTATGACCCCACCTTGCAACTCACCCTTGACGATTCAGGATGAAGCAATGACCAAAATGAATGGACTCAGTGGGATGAACGGACTGAATGGGATGAATGGATTGAATGGAATGAATGGGTTAAATGGAATGACAAATGGACACGTGGATCACCATCACTCTATGTACAATGGCAGGGCGGTGCGTCCAAGAAGAGATATGGCACCCTTACAATCACAGCCACCAGGAACTAGTGGCTATCCACGTTATGATCAATCATCATTTGGCTATCCATCAGATCCCACTGGTTATTGCAGtgCTCAACCTGATTACTATAGTCTTGCATATGGGAGGGCTGCCGTGTCTTATGAACCTGTCCCACAGACTATCATGGGCTACTCTTTCACAAGACAATACCACGATCCTCGCTTTGGATCAAGAAAGCCATACATTCCAGGCAATGATCCATTTGAAGAACCTggaaatgaaaacaatgataCAGCAACTGAATATGAGCCCATCCTTAGTTTTGGAGTTCTTAACAGGAAGGACACGACACTGTCTAGTGCCAGCAGTGGGGTCAGCAGTGGCTCCCCACTCAGCCACTCTCCTGCTGCTAGCCAATCGTCAAACTCCAGTTTATCACCGAGGCAACAGTCCCCTGTGGGGTGGCAACATGGGAGCGAGAATGACTTCAGCAACGTGAACCTTAAATTCTTAGAGGACAGTAGTACTCTGCCACCGCCCCCGGGTATCAACAATACTGCACCAATATGGTCACCTCATTGTGGCAACGAGAGGGGCAAGCTGTGGACCCGCTATAGTGTAGACTTCGACGAGTGGTCGAGGAAAGAGGAGCAGATAAAAAACGATGAGCAGTTTGCGCGAGCTCTTCAGGAGAAACTCCAACATGACAGCAAATCGTCGGAAATAATCGGCAGTGAATTGTTAGGATCGCGGGACAACAAAGACCAAGGCATTGATCAGGGGAGGAGAGGGCAGAACGTTCCAGATTGCGGCATAGGAATGGACAGCTTGGAGACTGAAGCAGAAATCAAGAAACGAAAGAAGGAAGAACACAGGCGTCTACTTCAGGAACGTAGAAATCTGCTTCAGCaacaggaaagagaaaaacaggAGCGAGATGATCGTATACTTGCCGAGGAACTAGCCTTAAATGATGCTCAACAAGCAGGGCTCTTCCCTGATCCTAGGTGCATCGTGAAACCCTATTCCAGTGTGATTTCCCGCGGGGCCCCCATGGGGATCGGTTTCGGCAGCCAGGGAAGCAGTGATGTTTCAGGGGAGTTAGATACGTTTAGCGGTTTTGGCAGCTTTCGTGGATCATGTGCATCTTCATTGGCTAATAATGACGAAGGCATAGATtcatcacagatgacgtcaggTTGCAGTGGAGACATACGTGTGCAAGAGTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q4VGL6	Roquin-1 OS=Mus musculus OX=10090 GN=Rc3h1 PE=1 SV=1
Q5TC82	Roquin-1 OS=Homo sapiens OX=9606 GN=RC3H1 PE=1 SV=1
P0C090	Roquin-2 OS=Mus musculus OX=10090 GN=Rc3h2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003562 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00642 all species →	zf-CCCH	Zinc finger C-x8-C-x5-C-x3-H type (and similar)	Family	Interproscan
PF18386 all species →	ROQ_II	Roquin II domain	Domain	Interproscan
PF14634 all species →	zf-RING_5	zinc-RING finger domain	Domain	Interproscan
PF21206 all species →	Roquin_1_2-like_ROQ	Roquin 1/2-like, ROQ domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000571 all species →	Domain	Zinc finger, CCCH-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR041523 all species →	Domain	Roquin II	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR048575 all species →	Domain	Roquin 1/2-like, ROQ domain	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR052249 all species →	Family	Roquin domain-containing protein	Interproscan
IPR036855 all species →	Homologous_superfamily	Zinc finger, CCCH-type superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13139 all species →	RING FINGER AND CCCH-TYPE ZINC FINGER DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0000288 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Interproscan
GO:0003725 all species →	Molecular Function	double-stranded RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0010494 all species →	Cellular Component	cytoplasmic stress granule	Interproscan
GO:0035613 all species →	Molecular Function	RNA stem-loop binding	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K15690	RC3H; RING finger and CCCH-type zinc finger domain-containing protein	-	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g7212.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

48TPM > 0

3Conditions

177.8Max TPM

72.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	71.04	160.85
whole organisms · low pH treatment	15	15	71.57	177.81
whole organisms · extra low pH treatment pH treatment	12	12	75.78	167.63

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	160.85
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	138.92
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	135.25
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	125.61
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	119.96
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	114.97
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	87.97
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	86.34
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	86.17
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	82.08
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	70.75
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	62.78
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	55.83
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	54.97
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	40.86
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	26.82
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	11.99
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	9.28
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	7.31
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	6.78
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	6.41
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	177.81
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	135.35
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	119.80
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	94.19
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	90.79
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	85.54
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	83.65
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	80.95
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	72.10
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	45.05
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	34.43
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	30.02
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	9.27
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	7.55
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	7.01
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	167.63
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	138.29
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	124.87
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	124.06
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	83.82
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	81.59
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	71.74
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	56.41
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	40.70
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	8.84
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	6.08
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	5.30

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.