Gene detail

Detailed information of g7545.t1 in Montipora capitata

Genomic Location: Sc0000176:96551...112127
NR annotation: XP_029188346.1, ribonucleoside-diphosphate reductase large subunit-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g7545.t1

atgtctgacaacatagatcttgagaatgaaactgaaactttggggacttacgtcattaaacgcaatcaaaagaagcaaggtgtatttctagacaagattacttctcgtatcgttaaacagtgctatggcttaaaaactgaattcgtggacgcgtttgctatcaccaagaaagttatttctggtatctaccctggagttcagacaactgagctggacaccttagctgccgagacagcggcttccatgacaactattcaccctgattatgctgtactggcagccagacttgaagtttctaaccttcacaaggaaaccaaaaaagtttttagtgaggtcatgactgacttgtacaagtatgtgaacccaaagaatgggaagcattctccacttatctcaaaggaaatctacgagatcattatggcaaatgctgatactctcaactctgccattatttatgatcgtgattatcattataactactttggttttaagactctgatgaggtcctacctgctgaaaataaatggtaaagtcgctgagcgcccccaacacatgctcatgagagtttcagtcggcattcatcaacatgatattagagctgctattgaaacttacaacctaatgtccgagaagtggttcacacatgcatctcccactctgtttaattctggaacatgcaagccacagttatcaagttgtttcctcctgaccatgacagacgatagcattgatggtatttatgaaacactcactacatgtgctaaaatttccaagtctgctggcggaattggtctcaatgtacataacataagagcttctggaagctatattgctgggaccaatggagtttcaaatggccttgttcccatgttacgtgtttataatgctactgcaagatatgttgatcagggaggaaacaagcgtcctggtgcctttgctgtgtacttagaaccatggcacaatgacatttttgatttcttggacttaaagaaaaatacaggaaaagaggaacagcgagccagagacttgttctacgcattgtggatccctgatcttttcatgcggcgttgtgaagctgatgggatgtggtcattgatgtgtcccaatgagtgtcctggtttacaagattgttggggagagaaatttgacaagctttatgaaagctatgagcaacagggaaagtttcgcaggcagatcaaggctcagaagttgtggtttgcaatcttggaggcacaaacagaaactggtactccctatatgctatataaagatgcatgcaacaggaaaagcaatcagcagaatcttgggacaatcaaatgcagcaatctctgtactgaaattgtagagtattcaagtccagatgaggttgctgtttgtaacttggcttctgttgcactcaataaatttgtgagtgatgaaactccaccacggtttgattttcaaaaactgagtgaggtcacccaggttgttactcgtaacttgaacaagatcattgacgttaactattatccagtgaaggaggctgaaaggtccaacaagagacacaggccaattggtattggtgtgcagggcatggctgatgcctttattttgctgaggtacccatttgaaagcaatgaagcaaaagaactgaacagaaaaatatttgagacaatttactatggagctttgaaggcatcatgccagttagccaaggaaaacggaccttacgagacatatgaaggttcacctgcaagtcatgggaaacttcaatatgatctctggggtgtaacaccgactgatttgtgggactgggcagcactcaaggcagatattaaaaaatatggattaagaaacagtctgctagttgcaccaatgccaacagcatctactgcacagatcctcggaaataatgagtcttttgaaccttacacaagtaacatctacacaaggcgtgtactttctggggaattccagattgtaaatcatcatctgttgaaggacttgactgagcggaaactctggaatgaaacgctaaaaaacaagctggtggctgctaatggatctattcagcacatggaggagattccagatgatctcaagccactgtacaagacagtctgggaaatctctcagaaggcactcattgatatggctgctgacagaggagccttcatcgaccagagccaatccttcaacgttttctttgctcaacccgacaattacaaactgacaagtatgcatttctatggctggaaaaagggcctcaaaacaggaatgtattaccttcgtacccgccctgcagctagtgcaattcagttcactgtggatcaagagtctctgaagaagacagccaagagcaaaaaggagaacgaagaagcccttgcttgctcattaaaaaatcctggtgcatgtgaaagctgcagtgggtaa

Transcript

g7545.t1

ATGTCTGACAACATAGATCTTGAGAATGAAACTGAAACTTTGGGGACTTACGTCATTAAACGCAATCAAAAGAAGCAAGGTGTATTTCTAGACAAGATTACTTCTCGTATCGTTAAACAGTGCTATGGCTTAAAAACTGAATTCGTGGACGCGTTTGCTATCACCAAGAAAGTTATTTCTGGTATCTACCCTGGAGTTCAGACAACTGAGCTGGACACCTTAGCTGCCGAGACAGCGGCTTCCATGACAACTATTCACCCTGATTATGCTGTACTGGCAGCCAGACTTGAAGTTTCTAACCTTCACAAGGAAACCAAAAAAGTTTTTAGTGAGGTCATGACTGACTTGTACAAGTATGTGAACCCAAAGAATGGGAAGCATTCTCCACTTATCTCAAAGGAAATCTACGAGATCATTATGGCAAATGCTGATACTCTCAACTCTGCCATTATTTATGATCGTGATTATCATTATAACTACTTTGGTTTTAAGACTCTGATGAGGTCCTACCTGCTGAAAATAAATGGTAAAGTCGCTGAGCGCCCCCAACACATGCTCATGAGAGTTTCAGTCGGCATTCATCAACATGATATTAGAGCTGCTATTGAAACTTACAACCTAATGTCCGAGAAGTGGTTCACACATGCATCTCCCACTCTGTTTAATTCTGGAACATGCAAGCCACAGTTATCAAGTTGTTTCCTCCTGACCATGACAGACGATAGCATTGATGGTATTTATGAAACACTCACTACATGTGCTAAAATTTCCAAGTCTGCTGGCGGAATTGGTCTCAATGTACATAACATAAGAGCTTCTGGAAGCTATATTGCTGGGACCAATGGAGTTTCAAATGGCCTTGTTCCCATGTTACGTGTTTATAATGCTACTGCAAGATATGTTGATCAGGGAGGAAACAAGCGTCCTGGTGCCTTTGCTGTGTACTTAGAACCATGGCACAATGACATTTTTGATTTCTTGGACTTAAAGAAAAATACAGGAAAAGAGGAACAGCGAGCCAGAGACTTGTTCTACGCATTGTGGATCCCTGATCTTTTCATGCGGCGTTGTGAAGCTGATGGGATGTGGTCATTGATGTGTCCCAATGAGTGTCCTGGTTTACAAGATTGTTGGGGAGAGAAATTTGACAAGCTTTATGAAAGCTATGAGCAACAGGGAAAGTTTCGCAGGCAGATCAAGGCTCAGAAGTTGTGGTTTGCAATCTTGGAGGCACAAACAGAAACTGGTACTCCCTATATGCTATATAAAGATGCATGCAACAGGAAAAGCAATCAGCAGaATCTTGGGACAATCAAATGCAGCAATCTCTGTACTGAAATTGTAGAGTATTCAAGTCCAGATGAGGTTGCTGTTTGTAACTTGGCTTCTGTTGCACTCAATAAATTTGTGAGTGATGAAACTCCACCACGGtttgattttcaaaaactgagTGAGGTCACCCAGGTTGTTACTCGTAACTTGAACAAGATCATTGACGTTAACTATTATCCAGTGAAGGAGGCTGAAAGGTCCAACAAGAGACACAGGCCAATTGGTATTGGTGTGCAGGGCATGGCTGATGCCTTTATTTTGCTGAGGTACCCATTTGAAAGCAATGAAGCAAAAGAACTGaacagaaaaatatttgagaCAATTTACTATGGAGCTTTGAAGGCATCATGCCAGTTAGCCAAGGAAAACGGACCTTACGAGACATATGAAGGTTCACCTGCAAGTCATGGGAAACTTCAATATGATCTCTGGGGTGTAACACCGACTGATTTGTGGGACTGGGCAGCACTCAAGGCAGATATTAAAAAATATGGATTAAGAAACAGTCTGCTAGTTGCACCAATGCCAACAGCATCTACTGCACAGATCCTCGGAAATAATGAGTCTTTTGAACCTTACACAAGTAACATCTACACAAGGCGTGTACTTTCTGGGGAATTCCAGATTGTAAATCATCATCTGTTGAAGGACTTGACTGAGCGGAAACTCTGGAATGAAACGCTAAAAAACAAGCTGGTGGCTGCTAATGGATCTATTCAGCACATGGAGGAGATTCCAGATGATCTCAAGCCACTGTACAAGACAGTCTGGGAAATCTCTCAGAAGGCACTCATTGATATGGCTGCTGACAGAGGAGCCTTCATCGACCAGAGCCAATCCTTCAACGTTTTCTTTGCTCAACCCGACAATTACAAACTGACAAGTATGCATTTCTATGGCTGGAAAAAGGGCCTCAAAACAGGAATGTATTACCTTCGTACCCGCCCTGCAGCTAGTGCAATTCAGTTCACTGTGGATCAAGAGTCTCTGAAGAAGACAGCCAAGAGCAAAAAGGAGAACGAAGAAGCCCTTGCTTGCTCATTAAAAAATCCTGGTGCATGTGAAAGCTGCAGTGGGTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P07742	Ribonucleoside-diphosphate reductase large subunit OS=Mus musculus OX=10090 GN=Rrm1 PE=1 SV=2
P23921	Ribonucleoside-diphosphate reductase large subunit OS=Homo sapiens OX=9606 GN=RRM1 PE=1 SV=1
Q5R919	Ribonucleoside-diphosphate reductase large subunit OS=Pongo abelii OX=9601 GN=RRM1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003633 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03477 all species →	ATP-cone	ATP cone domain	Domain	Interproscan
PF02867 all species →	Ribonuc_red_lgC	Ribonucleotide reductase, barrel domain	Family	Interproscan
PF00317 all species →	Ribonuc_red_lgN	Ribonucleotide reductase, all-alpha domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039718 all species →	Family	Ribonucleoside-diphosphate reductase large subunit	Interproscan
IPR005144 all species →	Domain	ATP-cone domain	Interproscan
IPR000788 all species →	Domain	Ribonucleotide reductase large subunit, C-terminal	Interproscan
IPR013346 all species →	Domain	Ribonucleotide reductase, class I, alpha subunit, C-terminal	Interproscan
IPR008926 all species →	Homologous_superfamily	Ribonucleotide reductase R1 subunit, N-terminal	Interproscan
IPR013509 all species →	Domain	Ribonucleotide reductase large subunit, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11573 all species →	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004748 all species →	Molecular Function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005971 all species →	Cellular Component	ribonucleoside-diphosphate reductase complex	Interproscan
GO:0009263 all species →	Biological Process	deoxyribonucleotide biosynthetic process	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
K10807	RRM1; ribonucleoside-diphosphate reductase subunit M1	EC:1.17.4.1	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g7545.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

400.8Max TPM

193.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	197.93	400.81
whole organisms · low pH treatment	15	15	198.80	313.18
whole organisms · extra low pH treatment pH treatment	12	12	178.58	321.72

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	400.81
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	334.76
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	312.66
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	293.38
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	284.27
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	279.06
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	273.21
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	262.31
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	258.53
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	245.78
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	228.81
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	217.67
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	210.90
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	87.46
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	84.05
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	82.04
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	79.95
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	62.07
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	54.77
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	53.66
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	50.43
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	313.18
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	311.07
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	301.95
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	285.86
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	284.36
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	281.63
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	276.40
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	232.80
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	186.34
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	118.91
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	106.52
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	101.08
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	66.00
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	61.84
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	54.10
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	321.72
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	310.00
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	296.33
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	259.27
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	244.03
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	217.32
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	104.99
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	102.86
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	101.54
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	70.23
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	57.90
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	56.80

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.