Gene detail

Detailed information of g7920.t1 in Montipora capitata

Genomic Location: Sc0000187:404654...429752
NR annotation: XP_044177134.1, LOW QUALITY PROTEIN: sister chromatid cohesion protein PDS5 homolog B-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g7920.t1

atgtttgtgcagtggcatgtcaggagagaagccatgatgtgtcttggcaagttgtataagaaagtaacaactggattgtgtgtggagagaattctgattggatgtttagtgcctgtgacactggaagctgatcagaagatgaaacgtttgctacatatttattgcaagcttgatgaggctgcagttagagtgcgaacagacattgtggaacttattgagctgtcagttcaagaaaaggtgtgctataaatttaacgtactttttcatagtgtaaaagaagccacgagaactatgttacatatcggttatatgtttgcattgcaatcgccggcgcctgtgtctgaagaaaatgaggcagtggtgttctcaaagataatctcacttgcaagagttttccctgatgctttcaaatttcaagagaacctcaagaaattacgggaaatgcttcaggaacccacactcagagagttatttaggaaaagtgttaaccctgatcttggatgttcagctgttttcaaggcagtgagtgatgtagtcttgaaggttggatccaagaatcctgtcctagagacagttaaaggtcttttggaccgtgctgcacctcttcttgttgatgaacagtgcatcaaggagctgtttaaactagtgaaagatgctgttgaggggctctcggatgaagaggatgacgagtatgagtggcatgaaagtgtaggggctagtcttgttgggaaaaaagggcttgctttgttgttggcattggctgctgtgtttccctctcaattccaaaatgaggacatttttcagcaacttttggtgttcctcaaaaacaaggatctagaaatagttgatgatgcacttaagatgcttgcattcactggtaatggcattcaaaaagttgacaagtctttggctaattattatcatccagtgttatctaaactagcactcaaaggaacgccgtgccaggccaaatactccttgcgatccattgcaaagatatcaccttcttcgtcacaaccttttgatcgtgtcttcgctaatcttgtcagttctttgagctatgactgtcctttactgttgacaactctgacagcactgggggaaattgcacttctggctccggcagtttttgaaaccgagaggccagctattgtgagagattttgttgtgaaggaattgctgatgaaagatagggtcaaagggattcgtcttttggtcaagtggctgaggggccaaaccagtaaccaagagctttgctcaaggccaatattcaagacatacattcaaccagttctcaggctacttgacagcttgcttgcatccaaaggagatttgcaacaacaaggccatgtgagtgctgctaactgttcaagacttcgtctggctgcggcctctggtatcatcaaaatagcacaggaacctcactgtactgaattcataacactggaagtcttccaaaagctgtcactagttatgcaagacccttgttatgaggtgcgtgacaaatttaccaagaagctacacaaagcagaggatttactgaaacttccattggagtatcttggaatatttgcccttgcagcaccagagcctgtcaaggaaagaaggaaccaggtgaagcaaatgatagcaaaaaatgttaagactagacgggattacttaaagcagcatacttctgcccaagcatgttcgcattccattttgccagagtatgcattaccctgtgtcattcacatgttggcgcatcatccagactttaagcgtgatgaccacgagaccttggttcagttcagagattatctttggttcttcatggagcccatcttagccaaagctgataattacagcttcttgaaaaaactagttgaaaatgtaaagcaaacaagagatgcacaagctccagatgatgaggaagtaaacaagaatctatacacagtctgtgatctggcactgggtcttaccttaaacaaggttcactcatttgtattaaaggaattccccggaaaccctgttttaccaaagaggttcttcgttccttcggagaagggcggcagtcccaacaccaggagctaccttccaaagggcttccaattcacatctggcaaggggccgaagaaagctggaactgtggaagcaaagtcagtacctttaaaagcgtcaaaaacggccggcaaacttcgagataagaaatcgcatgccaagtcccaaggaaaaagagatcaaaaaacaaaaagttcgaaaacgtcaaaaagtgcgttcaaggagaagataagggagatgcaagctgatgacgaagaagaagaagaggattctggaacgcaagagagtggatttgcgagccccgctgatgagcaaccgtcaccaaggaagagaggtcgacctgcgaattcctctgagaaaacggtatcaaagaaaccgaggaaagaatcctctgaggaatcctcatcctcgaaggaattatcttcgtctccctcaaagcaaagacttgtcaaacaaagtcgacagtcaccaagaaagaaggccaactcgccgccagaaagcccaaagcgccagtcgccgtctgcgactgcgcaaaagttgtcatcaaccaaaccgccatcaaggtga

Transcript

g7920.t1

ATGTTTGTGCAGTGGCATGTCAGGAGAGAAGCCATGATGTGTCTTGGCAAGTTGTATAAGAAAGTAACAACTGGATTGTGTGTGGAGAGAATTCTGATTGGATGTTTAGTGCCTGTGACACTGGAAGCTGATCAGAAGATGAAACGTTTGCTACATATTTATTGCAAGCTTGATGAGGCTGCAGTTAGAGTGCGAACAGACATTGTGGAACTTATTGAGCTGTCAGTTCAAGAAAAGGTGTGCTATAAATTTAACGTACTTTTTCATAGTGTAAAAGAAGCCACGAGAACTATGTTACATATCGGTTATATGTTTGCATTGCAATCGCCGGCGCCTGTGTCTGAAGAAAATGAGGCAGTGGTGTTCTCAAAGATAATCTCACTTGCAAGAGTTTTCCCTGATGCTTTCAAATTTCAAGAGAACCTCAAGAAATTACGGGAAATGCTTCAGGAACCCACACTCAGAGAGTTATTTAGGAAAAGTGTTAACCCTGATCTTGGATGTTCAGCTGTTTTCAAGGCAGTGAGTGATGTAGTCTTGAAGGTTGGATCCAAGAATCCTGTCCTAGAGACAGTTAAAGGTCTTTTGGACCGTGCTGCACCTCTTCTTGTTGATGAACAGTGCATCAAGGAGCTGTTTAAACTAGTGAAAGATGCTGTTGAGGGGCTCTCGGATGAAGAGGATGACGAGTATGAGTGGCATGAAAGTGTAGGGGCTAGTCTTGTTGGGAAAAAAGGGCTTGCTTTGTTGTTGGCATTGGCTGCTGTGTTTCCCTCTCAATTCCAAAATGAGGACATTTTTCAGCAACTTTTGGTGTTCCTCAAAAACAAGGATCTAGAAATAGttGATGATGCACTTAAGATGCTTGCATTCACTGGTAATGGCATTCAAAAAGTTGACAAGTCTTTGGCTAAttATTATCATCCAGTGTTATCTAAACTAGCACTCAAAGGAACGCCGTGCCAGGCCAAATACTCCTTGCGATCCATTGCAAAGATATCACCTTCTTCGTCACAACCTTTTGATCGTGTCTTCGCTaatCTTGTCAGTTCTTTGAGCTATGACTGTCCTTTACTGTTGACAACTCTGACAGCACTGGGGGAAATTGCACTTCTGGCTCCGGCAGTTTTTGAAACCGAGAGGCCAGCTATTGTGAGAGATTTTGTTGTGAAGGAATTGCTGATGAAAGATAGGGTCAAAGGGATTCGTCTTTTGGTCAAGTGGCTGAGGGGCCAAACCAGTAACCAAGAGCTTTGCTCAAGGCCAATATTCAAGACATACATTCAACCAGTTCTCAGGCTACTTGACAGCTTGCTTGCATCCAAAGGAGATTTGCAACAACAAGGCCATGTGAGTGCTGCTAACTGTTCAAGACTTCGTCTGGCTGCGGCCTCTGGTATCATCAAAATAGCACAGGAACCTCACTGTACTGAATTCATAACACTGGAAGTCTTCCAAAAGCTGTCACTAGTTATGCAAgaCCCTTGTTATGAGGTGCGTGACAAATTTACCAAGAAGCTACACAAAGCAGAGGATTTACTGAAACTTCCATTGGAGTATCTTGGAATATTTGCCCTTGCAGCACCAGAGCCTGTCAAGGAAAGAAGGAACCAGgtGAAGCAAATGATAGCAAAAAATGTTAAGACTAGACGGGATTACTTAAAGCAGCATACTTCTGCCCAAGcATGTTCGCATTCCATTTTGCCAGAGTATGCATTACCCTGTGTCATTCACATGTTGGCGCATCATCCAGACTTTAAGCGTGATGACCACGAGACCTTGGTTCAGTTCAGAGATTATCTTTGGTTCTTCATGGAGCCCATCTTAGCCAAAGCTGATAATTACAGCTTCTTGAAAAAACTAGTTGAAAATGTAaagcaaacaagagatgcacaAGCTCCAGATGATGAGGAAGTAAACAAGAATCTATACACAGTCTGTGATCTGGCACTGGGTCTTACCTTAAACAAGGTTCACTCATTTGTATTAAAGGAATTCCCCGGAAACCCTGTTTTACCAAAGAGGTTCTTCGTTCCTTCGGAGAAGGGCGGCAGTCCCAACACCAGGAGCTACCTTCCAAAGGGCTTCCAATTCACATCTGGCAAGGGGCCGAAGAAAGCTGGAACTGTGGAAGCAAAGTCAGTACCTTTAAAAGCGTCAAAAACGGCCGGCAAACTTCGAGATAAGAAATCGCATGCCAAGTCCCAAGGAAAAAGAGATCAAAAAACAAAAAGTTCGAAAACGTCAAAAAGTGCGTTCAAGGAGAAGATAAGGGAGATGCAAGCTgatgacgaagaagaagaagaggattCTGGAACGCAAGAGAGTGGATTTGCGAGCCCCGCTGATGAGCAACCGTCACCAAGGAAGAGAGGTCGACCTGCGAATTCCTCTGAGAAAACGGTATCAAAGAAACCGAGGAAAGAATCCTCTGAGGAATCCTCATCCTCGAAGGAATTATCTTCGTCTCCCTCAAAGCAAAGACTTGTCAAACAAAGTCGACAGTCACCAAGAAAGAAGGCCAACTCGCCGCCAGAAAGCCCAAAGCGCCAGTCGCCGTCTGCGACTGCGCAAAAGTTGTCATCAACCAAACCGCCATCAAGGTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5F3U9	Sister chromatid cohesion protein PDS5 homolog B OS=Gallus gallus OX=9031 GN=PDS5B PE=2 SV=3
Q498H0	Sister chromatid cohesion protein PDS5 homolog B-A OS=Xenopus laevis OX=8355 GN=pds5b-a PE=1 SV=1
Q4VA53	Sister chromatid cohesion protein PDS5 homolog B OS=Mus musculus OX=10090 GN=Pds5b PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003692 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF20168 all species →	PDS5	Sister chromatid cohesion protein PDS5 protein	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039776 all species →	Family	Sister chromatid cohesion protein Pds5	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12663 all species →	ANDROGEN INDUCED INHIBITOR OF PROLIFERATION AS3 / PDS5-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0007064 all species →	Biological Process	mitotic sister chromatid cohesion	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
K11267	PDS5; sister chromatid cohesion protein PDS5	-	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g7920.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

126.8Max TPM

48.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	45.08	125.05
whole organisms · low pH treatment	15	15	53.15	126.83
whole organisms · extra low pH treatment pH treatment	12	12	48.54	115.93

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	125.05
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	104.24
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	98.09
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	76.46
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	73.74
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	69.41
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	64.70
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	57.56
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	54.20
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	33.52
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	31.88
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	28.86
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	26.67
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	22.54
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	21.97
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	20.09
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	11.52
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	8.53
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	8.46
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	6.31
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	2.92
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	126.83
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	115.21
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	107.07
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	70.67
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	69.44
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	64.80
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	63.06
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	53.94
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	40.62
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	22.79
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	22.55
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	21.52
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	7.34
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	6.70
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	4.69
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	115.93
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	104.08
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	81.87
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	64.33
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	63.15
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	60.77
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	27.60
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	26.61
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	24.09
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	6.83
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	3.84
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	3.38

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.