Gene detail

Detailed information of g10593.t1 in Montipora capitata

Genomic Location: Sc0000300:129705...172595
NR annotation: XP_044184368.1, structural maintenance of chromosomes flexible hinge domain-containing protein 1-like isoform X2 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g10593.t1

atggagttacgagatgttgatgatgacatgcaaactcgttatatcaggacagctgcttctgtgtttgaattctgtgcacatccagagtcaggcggtgttgttgagggcatcttgcgttaccatccatttctttatgatagagagacgtatccttctcttgatggggaattcccagttgttgaaactgctgaggagttaactgaatcagtggaaagagatagcagggcaccaagaggaaaccgtccaatatttgagtgttattggaatggacgacttatcccatacagtactatagatatgcttgactggtgccaacctccaaggaaatcagttattcctttggaatgttataacagattttcgggttgtctttggacaaatgatgcttttcaagtgagcacaaacaagttgacctttatggatttggaagtgaaaatcagagacaagaacaccatgttcagcaggatcattttgggacaggagcaaagagtaaacatttccagagcatttcttgactgggtgagagagagtcatgaaaaccacgacaagcaggagccggtgtctctgtatggagacagaaagttcttttccttggctaagttggaccgttcaataacccttgcctcagtcaagaaatttgtggaagatgaagaggcaaagttgcccagtaaattggtgatagaatggccagagaacaacaagcttgaaccgaactctaaaatccctgcaggaaccaccataggtgccatgaaggtagatattgtgaatggaaaaggtgaatcggtcaacaaacttcctggtgataggagaaggttgttggtggaattaaaggtcttgtggcatgaaaacatcacccatcttgggccccacactctccagctgcaagttttgctcagtgacagttcaactgcaccatctatgaagagccttcccagtcattgtatcaatttcactgtcacaggagttttcttttatgctaagttttatgatctttttactgtagaggctcatccaaataagttcactgttggaatgttggaaacccctttaagagttggtgtaccatttcagattccacttaacctacttgatgaatttaacaatccatcaaaattgtcagaagaggttactccagttttgagtgcaagtgggttggagttgactcatcaaggaacaactgtgaaagttaacagtctcattgtcaaaggcgtggtcgctttaggctctgtatcatcccatgctggaaaggattttaatctcaaaattgctttacctggtctcgatgaaggctctcaaagtttaaagatcaggctgcttccaggtccaccagagttattagctgtgtccccaagtgaccctgagatcacaattgaaaacaacaactcccttgatctacaagtccaggttcaggataaagctggaaacatcactgttcagcccaggttgaatgttgtttgcaagctgaccggactaccaagtttgccaacctatgttggagactgcagctcttctggcaaggcaacactttcgggtcctgacatctgcctaaagcaaatcaccagtgaaacaaaactcaaggccaggattgaattgcagcatcacaagaaagttgctccagtcgaaaagaccatcattgtgacacccagtagaaaagcggctgtcctggaagtgttttatgaagcagatgacgctgaagaaaagaagaagcttgaagatggacaggaattgccatgtactgctgggcaaacagtgtctggattgacctttagagttctagatgaaggacagagagaattagccattgacagcttggtggccaacagattcaaggtcaactggaccccaaaagtatcaaaagatctcatcaagcaaggaatccttccagatgtcaagttacccagtcacgttcttccagagtttcatgtttcatcagatggacttcgagaaagtgaggtccagctaggcttcactgctgatggaaatattgtcatcaagaatgttcagtttgaggatggtcctttgggtcatcgagaacttgctatgaaatggaaagaattgatatgctatcaaaggatagaggttatttcaggtccgccagcaaagcttaagattcttgatatggatctctctgagcccctttgtgtgtttaatgacagcagaatgccacatcccgtcaccgttcaactgtgtgataagcttggaaatgcttcggatgaggagaatgtcaaagttgtgctcaattatgatcgaggactgaatttgactccgacaccagctcaacagaagacggatagcaaggggcaagctacatttggacatctcactgtcagtgcatccaaaggaatgtatggaataagaatcaaagctctccttggaagaacgtctttaaatgcaccaactattaacgtcagagtggaacccgacccttcaaaagctgtggatctttctgtaacgttcaactccaaggcaccttgtgttgtgggagagttgttgccagctgtgtcagcgcatgtcgtaggagaggatgatgctgtcatgaaactgtcaagttctagagatatagttttaaagatatggcactcaacggacggaccagtatcagacaaacctcctgccagggccacaacgttgtatccatcaaagccgaaaccaaccgataaggacggagaattttacttcagggatctcaaggtgccagacttagcaggagcctattgcatggtggtgcagtttgggtccgaaggacaagtgacactctcaagtaaaccgatgacattcacagcgaaagctgggatgcctgtgaagcttgaacctgaatcgattcctgccactcccaccgataagtttgataatctgactggtgagactttgcgagggaaagtggtaataaacgtgagctcctcttcggaaggaattgacgagattcccgcattggctggcaatgtgtactccatggaggttcctcttgtaaagggtgtggccacagtacaaaacctactcatgcaagaaaacactgccggaaaggatggacaggaatatttactaaacttcagtgctcagatccctcctaatgcatcgcttcatcctattccaccattcacccttgcttttctattctacaatgagatagacgttagtgttttgtttgctgttttagtttcagtacacgaagcgtccttacaagaacagaaaatgagaggagagctcaggaaacagaatgtagctgcgagcagtttggcttcagtcgcccatttagctcaagtggtggatgatgacgtagcgcgagtgttatcgtggcacatggcttctgatatggactgtgttgttactctcaccactgaaaaggctaagcaagtgtaccgtgattcaaatggtcaacaacaagttcttcccttggattccatctttagacggagtttacccgaatggaacagacccctgcctcatgtacgcggtggtcaaagtagatccaacccttctggcaaccctgtgtatgcaagagatatgctgctctttccaacagaggctgataactgcaagctagtgtttggcatgttgctcggggatacattgatccttgatgaccttgactgtgctaacaaatacaggcaagaagttgtgaaatacacccactgtcccacgattttaacaagatgcggagatcgcatcagaagtaatgagcaattgcaagcatacaaagtatccttcactaaacacacacaagctaaggaagaacttgcccaacaactacagcacggtcaaacagaagagatgaaagtgaaacatcgagagtgcagagaagccgaaaatcagttacgcttgatagaagagcgtcttggcatgacacccacacaatacaatatgcccccaagtccagccacaatgttactaacagaaataaatacacctccgacgaggaccgcgacatctcgtcggtcaggcgctcgggcgtcagcggcagctaccgcctcaccgactttgtcatcggcgccaatcgtcaacggcacgaacagcacttcatctaacatttctccaaggacaaggcgaggtgctccgttgcctcccgaagatgtacgcactagtaaacgaactcggagatga

Transcript

g10593.t1

ATGGAGTTACGAGATGTTGATGATGACATGCAAACTCGTTATATCAGGACAGCTGCTTCTGTGTTTGAATTCTGTGCACATCCAGAGTCAGGCGGTGTTGTTGAGGGCATCTTGCGTTACCATCCATTTCTTTATGATAGAGAGACGTATCCTTCTCTTGATGGGGAATTCCCAGTTGTTGAAACTGCTGAGGAGTTAACTGAATCAGTGGAAAGAGATAGCAGGGCACCAAGAGGAAACCGTCCAATATTTGAGTGTTATTGGAATGGACGACTTATCCCATACAGTACTATAGATATGCTTGACTGGTGCCAACCTCCAAGGAAATCAGTTATTCCTTTGGAATGTTATAACAGATTTTCGGGTTGTCTTTGGACAAATGATGCTTTTCAAGTGAGCACAAACAAGTTGACCTTTATGGATTTGGAAGTGAAAATCAGAGACAAGAACACCATGTTCAGCAGGATCATTTTGGGACAGGAGCAAAGAGTAAACATTTCCAGAGCATTTCTTGACTGGGTGAGAGAGAGTCATGAAAACCACGACAAGCAGGAGCCGGTGTCTCTGTATGGAGACAGAAAGTTCTTTTCCTTGGCTAAGTTGGACCGTTCAATAACCCTTGCCTCAGTCAAGAAATTTGTGGAAGATGAAGAGGCAAAGTTGCCCAGTAAATTGGTGATAGAATGGCCAGAGAACAACAAGCTTGAACCGAACTCTAAAATCCCTGCAGGAACCACCATAGGTGCCATGAAGGTAGATATTGTGAATGGAAAAGGTGAATCGGTCAACAAACTTCCTGGTGATAGGAGAAGGTTGTTGGTGGAATTAAAGGTCTTGTGGCATGAAAACATCACCCATCTTGGGCCCCACACTCTCCAGCTGCAAGTTTTGCTCAGTGACAGTTCAACTGCACCATCTATGAAGAGCCTTCCCAGTCATTGTATCAATTTCACTGTCACAGGAGTTTTCTTTTATGCTAAGTTTTATGATCTTTTTACTGTAGAGGCTCATCCAAATAAGTTCACTGTTGGAATGTTGGAAACCCCTTTAAGAGTTGGTGTACCATTTCAGATTCCACTTAACCTACTTGATGAATTTAACAATCCATCAAAATTGTCAGAAGAGGTTACTCCAGTTTTGAGTGCAAGTGGGTTGGAGTTGACTCATCAAGGAACAACTGTGAAAGTTAACAGTCTCATTGTCAAAGGCGTGGTCGCTTTAGGCTCTGTATCATCCCATGCTGGAAAGGATTTTAATCTCAAAATTGCTTTACCTGGTCTCGATGAAGGCTCTCAAAGTTTAAAGATCAGGCTGCTTCCAGGTCCACCAGAGTTATTAGCTGTGTCCCCAAGTGACCCTGAGATCACAATTGAAAACAACAACTCCCTTGATCTACAAGTCCAGGTTCAGGATAAAGCTGGAAACATCACTGTTCAGCCCAGGTTGAATGTTGTTTGCAAGCTGACCGGACTACCAAGTTTGCCAACCTATGTTGGAGACTGCAGCTCTTCTGGCAAGGCAACACTTTCGGGTCCTGACATCTGCCTAAAGCAAATCACCAGTGAAACAAAACTCAAGGCCAGGATTGAATTGCAGcatcaCAAGAAAGTTGCTCCAGTCGAAAAGACCATCATTGTGACACCCAGTAGAAAAGCGGCTGTCCTGGAAGTGTTTTATGAAGCAGATGACgctgaagaaaagaagaagcttGAAGATGGACAGGAATTGCCATGTACTGCTGGGCAAACAGTGTCTGGATTGACCTTTAGAGTTCTAGATGAAGGACAGAGAGAATTAGCCATTGACAGCTTGGTGGCCAACAGATTCAAGgtCAACTGGaccccaaaagtatcaaaagaTCTCATCAAGCAAGGAATCCTTCCAGATGTCAAGTTACCCAGTCACGTTCTTCCAGAGTTTCATGTTTCATCAGATGGACTTCGAGAAAGTGAGGTCCAGCTAGGCTTCACTGCTGATGGAAATATTGTCATCAAGAATGTTCAGTTTGAGGATGGTCCTTTGGGTCATCGAGAACTTGCTATGAAATGGAAAGAATTGATATGCTATCAAAGGATAGAGGTTATTTCAGGTCCGCCAGCAAAGCTTAAGATTCTTGATATGGATCTCTCTGAGCCCCTTTGTGTGTTTAATGACAGCAGAATGCCACATCCCGTCACCGTTCAACTGTGTGATAAGCTTGGAAATGCTTCGGATGAGGAGAATGTCAAAGTTGTGCTCAATTATGATCGAGGACTGAATTTGACTCCGACACCAGCTCAACAGAAGACGGATAGCAAGGGGCAAGCTACATTTGGACATCTCACTGTCAGTGCATCCAAAGGAATGTATGGAATAAGAATCAAAGCTCTCCTTGGAAGAACGTCTTTAAATGCACCAACTATTAACGTCAGagTGGAACCCGACCCTTCAAAAGCTGTGGATCTTTCTGTAACGTTCAACTCCAAGGCACCTTGTGTTGTGGGAGAGTTGTTGCCAGCTGTGTCAGCGCATGTCGTAGGAGAGGATGATGCTGTCATGAAACTGTCAAGTTCTAGAGATATAGTTTTAAAGATATGGCACTCAACGGACGGACCAGTATCAGACAAACCTCCTGCCAGGGCCACAACGTTGTATCCATCAAAGCCGAAACCAACCGATAAGGACGGAGAATTTTACTTCAGGGATCTCAAGGTGCCAGACTTAGCAGGAGCCTATTGCATGGTGGTGCAGTTTGGGTCCGAAGGACAAGTGACACTCTCAAGTAAACCGATGACATTCACAGCGAAAGCTGGGATGCCTGTGAAGCTTGAACCTGAATCGATTCCTGCCACTCCCACCGATAAGTTTGATAATCTGACTGGTGAGACTTTGCGAGGGAAAGTGGTAATAAACGTGAGCTCCTCTTCGGAAGGAATTGACGAGATTCCCGCATTGGCTGGCAATGTGTACTCCATGGAGGTTCCTCTTGTAAAGGGTGTGGCCACAGTACAAAACCTACTCATGCAAGAAAACACTGCCGGAAAGGATGGACAGGAATATTTACTAAACTTCAGTGCTCAGATCCCTCCTAATGCATCGCTTCATCCTATTCCACCATTCACCCTTGCTTTTCTATTCTACAATGAGATAGACGTTAGtgttttgtttgctgttttagTTTCAGTACACGAAGCGTCCTTACAAGAACAGAAAATGAGAGGAGAGCTCAGGAAACAGAATGTAGCTGCGAGCAGTTTGGCTTCAGTCGCCCATTTAGCTCAAGTGGTGGATGATGACGTAGCGCGAGTGTTATCGTGGCACATGGCTTCTGATATGGACTGTGTTGTTACTCTCACCACTGAAAAGGCTAAGCAAGTGTACCGTGATTCAAATGGTCAACAACAAGTTCTTCCCTTGGATTCCATCTTTAGACGGAGTTTACCCGAATGGAACAGACCCCTGCCTCATGTACGCGGTGGTCAAAGTAGATCCAACCCTTCTGGCAACCCTGTGTATGCAAGAGATATGCTGCTCTTTCCAACAGAGGCTGATAACTGCAAGCTAGTGTTTGGCATGTTGCTCGGGGATACATTGATCCTTGATGACCTTGACTGTGCTAACAAATACAGGCAAGAAGTTGTGAAATACACCCACTGTCCCACGATTTTAACAAGATGCGGAGATCGCATCAGAAGTAATGAGCAATTGCAAGCATACAAAGTATCCTTCACTAAACACACACAAGCTAAGGAAGAACTTGCCCAACAACTACAGCACGGTCAAACAGAAGAGATGAAAGTGAAACATCGAGAGTGCAGAGAAGCCGAAAATCAGTTACGCTTGATAGAAGAGCGTCTTGGCATGACACCCACACAATACAATATGCCCCCAAGTCCAGCCACAATGTTACTAACAGAAATAAATACACCTCCGACGAGGACCGCGACATCTCGTCGGTCAGGCGCTCGGGCGTCAGCGGCAGCTACCGCCTCACCGACTTTGTCATCGGCGCCAATCGTCAACGGCACGAACAGCACTTCATCTAACATTTCTCCAAGGACAAGGCGAGGTGCTCCGTTGCCTCCCGAAGATGTACGCACTAGTAAACGAACTCGGAGATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6P5D8	Structural maintenance of chromosomes flexible hinge domain-containing protein 1 OS=Mus musculus OX=10090 GN=Smchd1 PE=1 SV=2
A6NHR9	Structural maintenance of chromosomes flexible hinge domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SMCHD1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002050 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06470 all species →	SMC_hinge	SMC proteins Flexible Hinge Domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010935 all species →	Domain	SMCs flexible hinge	Interproscan
IPR038892 all species →	Family	Structural maintenance of chromosomes flexible hinge domain-containing protein 1	Interproscan
IPR036277 all species →	Homologous_superfamily	SMCs flexible hinge superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22640 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005694 all species →	Cellular Component	chromosome	Interproscan
GO:0051276 all species →	Biological Process	chromosome organization	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	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
K23113	SMCHD1; structural maintenance of chromosomes flexible hinge domain-containing protein 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 g10593.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

287.9Max TPM

96.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	92.09	239.11
whole organisms · low pH treatment	15	15	106.14	287.86
whole organisms · extra low pH treatment pH treatment	12	12	90.95	210.97

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	239.11
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	224.13
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	185.95
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	114.33
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	105.77
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	102.30
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	102.20
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	99.38
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	96.29
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	94.27
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	86.02
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	82.17
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	80.53
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	67.66
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	44.04
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	43.00
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	40.64
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	35.97
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	32.87
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	30.79
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	26.51
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	287.86
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	214.39
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	209.73
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	105.95
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	104.54
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	102.90
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	89.14
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	85.56
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	85.53
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	81.15
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	73.07
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	59.76
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	32.01
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	31.63
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	28.89
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	210.97
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	175.91
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	114.85
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	90.38
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	82.00
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	80.99
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	76.59
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	75.44
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	72.62
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	39.07
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	36.75
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	35.82

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.