Gene detail

Detailed information of XP_032236023.2 in Nematostella vectensis

Genomic Location: NC_064037.1:13851865...13868484
NR annotation: XP_032236023.2, FACT complex subunit SSRP1 isoform X2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5510940

ATGGCTTCGGAGGGTTTGGAGTATAACGAAGTGTCACTGCTGGTTCGCGGTGCTTTGAATTCAGGCAGACTAAAGCTACATAAAAGTGGAGCTGTGTTCAAGGCCAGTAAGACTGGTCGTGTTGACCAGTTCAGTAAAGACGACATTGAGTCAGCTCACTGGTTGAGAGTAGCATGCGGGCAGGAGCTAAAGATTGTCTTGAAGAGTGGACTTCAGTTTAGATTTGATGGTTTCAAAGAGAGTGATTTTGCTAATTTATCAGAGTTTCTAAAATCATTTTTTGGAGTCAAGTTAGAGGAGATGGAACTATCAGTCAAGGGTTGGAACTGGGGTACTGCCACTTTCAATGGCTCAGCACTTGCGTTTGAAGTGGATAAAAAGCCAGCGTTTGAAATCCCACTGAAAGATGTATCTCAAGCTACAACAGCAGGTAACAATGAAGTGACGTTAGAGTTCCATCAGCATGATGATGCAGAGGTGGCGCTCATGGAGATGAGGTTTTATATCCCTACTCCGGCCGACAGCACCGACCCTAACCCCGTCACGACCTTCCATGAACATGTCCTTTCAAAGGCAGATATTATACAGATCACTGGGGACGCAATTGTTACAATACCTGATGTCGCCTGTCTCACACCAAGAGGTCGCTACACAATGAAAATATTTCCGACATTTGTACAGCTTCATGGAAAAACATATGACTACAAAATTCCCTATACTACAATACTACGGATATTCTTGCTGCCTCACAAGGATCACATGTTCTTTGTGGTCAGTATGGACCCTCCCATCAAACAAGGACAGACTCGGTACCCATTCCTTATCACACGCTTTGACAAAGATGAGCATTTCGATGTGAAACTCAACATCTCAGAAGAGGAGATGAAGGAGAAATATGATGGGAAGATTGAGAAGGAGATGAGTGGAGCTATTTATGAGATCATCAGTAGACTGATGAAGGCTGTTGTTGGCAAGAAAATCACTGTGCCTGGTACATTCAAAAGTCACCAGGGCGTCAGCTGTATCACATGTTCTCACCGGGCTGGCAGTGGACTGCTATATCCTCTGGAGAGGGGTTTTATCTTCATCCACAAGCCTCCAGTCCACGTCAGATTTGATGAGATTTCTGCTGTCAACTTTGCCCGTGTGGCAGGTGCTGGAGGTCACAGTCGTTCCTTTGACTTTGAGCTGCAGACAAAGAATGGGACTACTATTGTGTTCAGTAGTATTGAAAGGGAAGAATATGGGAGACTATTTGACTTTGTACGAGACAAGAAGCTACGTATCAAGAACACTGGAAAGGCAACAACAAAGAGTACTAAGGAAAAAAATATTGATGATGATTTGATGGGATCAGATGATGATGAGCATGATGCTTACCTAGAGACCGTCAAAGCAGAGGCTGCAGCAAGGGATGAAGACGATGATGAGTCCGAAGATGAAGATTCAGATGATGAGTCGTTTGCGCCTGAGGGCAGTGGTGATGACCAAGACGTCAGGGAAGAGTTCGAAAGTGAACCCTCTTCTTCTGAAGCGTCGGGATCAGATTCAGAGGGAGAGAGTAAAAAGAAGAAAAAGGAGAAACCAGAAAAGAAGCGAAAAGCAGAAAAACCACCAAAGTCCCCAAAGAAAAAGGCAAAAACCGCGAGCTTCGTTGAGACAGGCGAAAAAGGCAAGAAGGGTGGAAAGAAGAAGAAAGATCCTAACGCGCCCAAGAGAGCTATGAGTGCCTACATGCTTTGGCTGAATGATACTCGTCAGGAGATCAAGGACAAGAACCCGGGAATATCCGTGACAGAGGTGTCTAAAGTGGCGGGCGAGATGTGGAAGAATCTTACAGATAAATCGAAATGGGAAGAAAAGGCAGCGATCGAAAAACAGAAATATGTACAGAGGATGAAAGAGTACAACGAAAACAAGAAAAATGACGAGGAAGAGAGTCCCAAGAAGAAATCTCCATCGAAAAAAGCTTCCAAGGCTCCCAAAGAAGAGAAGAGCCCATCTCCCCGAAAAAGCCTGGACAACAACCAGAAGTTCAAAAGCGCTGAGTTTGTTGAATCCAGCGGAGATTCGTCAGATTCCGAGGCCGAAAAGAAGAAGGGGAAAGGCAAAAAGTCAGCGAGTAAAAGCAAGAAAAAGAAGGAAGAGTCTTCAGAAGACGAGTCTATGGAGGAGGAGTCAGAAGAAGAGATGAGTGAGGGTGCGTCCGATTCAGACTGA

Transcript

rna-XM_032380132.2

GCACGCGACCGCGGAATCAAAGTTtcatccgccattttgaatccAACACGAACTTGTACAAAACTATTGGTGCCCTTAGCGATCGAATAAAGTCTGAGCCAAGGAATTGATGCTATGGCTTCGGAGGGTTTGGAGTATAACGAAGTGTCACTGCTGGTTCGCGGTGCTTTGAATTCAGGCAGACTAAAGCTACATAAAAGTGGAGCTGTGTTCAAGGCCAGTAAGACTGGTCGTGTTGACCAGTTCAGTAAAGACGACATTGAGTCAGCTCACTGGTTGAGAGTAGCATGCGGGCAGGAGCTAAAGATTGTCTTGAAGAGTGGACTTCAGTTTAGATTTGATGGTTTCAAAGAGAGTGATTTTGCTAATTTATCAGAGTTTCTAAAATCATTTTTTGGAGTCAAGTTAGAGGAGATGGAACTATCAGTCAAGGGTTGGAACTGGGGTACTGCCACTTTCAATGGCTCAGCACTTGCGTTTGAAGTGGATAAAAAGCCAGCGTTTGAAATCCCACTGAAAGATGTATCTCAAGCTACAACAGCAGgtaACAATGAAGTGACGTTAGAGTTCCATCAGCATGATGATGCAGAGGTGGCGCTCATGGAGATGAGGTTTTATATCCCTACTCCGGCCGACAGCACCGACCCTAACCCCGTCACGACCTTCCATGAACATGTCCTTTCAAAGGCAGATATTATACAGatcactggggacgcaattgTTACAATACCTGATGTCGCCTGTCTCACACCAAGagGTCGCTACACAATGAAAATATTTCCGACATTTGTACAGCTTCATGGAAAAACATATGACTACAAAATTCCctatactacaatactacggATATTCTTGCTGCCTCACAAGGATCACATGTTCTTTGTGGTCAGTATGGACCCTCCCATCAAACAAGGACAGACTCGGTACCCATTCCTTATCACACGCTTTGACAAAGATGAGCATTTCGATGTGAAACTCAACATCTCAGAAGAGGAGATGAAGGAGAAATATGATGGGAAGATTGAGAAGGAGATGAGTGGAGCTATTTATGAGATCATCAGTAGACTGATGAAGGCTGTTGTTGGCAAGAAAATCACTGTGCCTGGTACATTCAAAAGTCACCAGGGCGTCAGCTGTATCACATGTTCTCACCGGGCTGGCAGTGGACTGCTATATCCTCTGGAGAGGGGTTTTATCTTCATCCACAAGCCTCCAGTCCACGTCAGATTTGATGAGATTTCTGCTGTCAACTTTGCCCGTGTGGCAGGTGCTGGAGGTCACAGTCGTTCCTTTGACTTTGAGCTGCAGACAAAGAATGGGACTACTATTGTGTTCAGTAGTATTGAAAGGGAAGAATATGGGAGACTATTTGACTTTGTACGAGACAAGAAGCTACGTATCAAGAACACTGGAAAGGCAACAACAAAGAGTactaaggaaaaaaatattgatgatgatttgaTGGGATCAGATGATGATGAGCATGATGCTTACCTAGAGACCGTCAAAGCAGAGGCTGCAGCAAGGGATGAAGACGATGATGAGTCCGAAGATGAAGATTCAGATGATGAGTCGTTTGCGCCTGAGGGCAGTGGTGATGACCAAGACGTCAGGGAAGAGTTCGAAAGTGAACCCTCTTCTTCTGAAGCGTCGGGATCAGATTCAGAGGGAGAgagtaaaaagaagaaaaaggagaaACCAGAAAAGAAGCGAAAAGCAGAAAAACCACCAAAGTCCCCAAAGAAAAAGGCAAAAACCGCGAGCTTCGTTGAGACAGGCGAAAAAGGCAAGAAGGGtggaaagaagaagaaagatcCTAACGCGCCCAAGAGAGCTATGAGTGCCTACATGCTTTGGCTGAATGATACTCGTCAGGAGATCAAGGACAAGAACCCGGGAATATCCGTGACAGAGGTGTCTAAAGTGGCGGGCGAGATGTGGAAGAATCTTACAGATAAATCGAAATGGGAAGAAAAGGCAGCGATcgaaaaacagaaatatgTACAGAGGATGAAAGAGTACAacgaaaacaagaaaaatgacGAGGAAGAGAGTCCCAAGAAGAAATCTCCATCGAAAAAAGCTTCCAAGGCTCCCAAAGAAGAGAAGAGCCCATCTCCCCGAAAAAGCCTGGACAACAACCAGAAGTTCAAAAGCGCTGAGTTTGTTGAATCCAGCGGAGATTCGTCAGATTCCGAGGCCGAAAAGAAGAAGGGGAAAGGCAAAAAGTCAGCGAGTAAAAGCAAGAAAAAGAAGGAAGAGTCTTCAGAAGACGAGTCTATGGAGGAGGAGTCAGAAGAAGAGATGAGTGAGGGTGCGTCCGATTCAGACTGATGCTGGTTAACCAGACGGGCCAGGACGAACAAGCATCTCGATCTGTTTGAGTCATTGAACATTGCTTAATCGTAGATCCTAAACTCAGCTTTATAAATATTGTCAAAGTGCTTCTAAGATATTTGCTTGTGAATAAACCAATTTTATTGTGAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q04678	FACT complex subunit SSRP1 OS=Gallus gallus OX=9031 GN=SSRP1 PE=2 SV=2
Q08943	FACT complex subunit SSRP1 OS=Mus musculus OX=10090 GN=Ssrp1 PE=1 SV=2
Q9W602	FACT complex subunit SSRP1 OS=Xenopus laevis OX=8355 GN=ssrp1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005729 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21103 all species →	PH1_SSRP1-like	SSRP1 PH domain	Domain	Interproscan
PF08512 all species →	Rttp106-like_middle	Histone chaperone Rttp106-like, middle domain	Domain	Interproscan
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan
PF03531 all species →	SSrecog	Structure-specific recognition protein (SSRP1)	Domain	Interproscan
PF17292 all species →	POB3_N	POB3-like N-terminal PH domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan
IPR048993 all species →	Domain	FACT complex subunit SSRP1-like, first PH domain	Interproscan
IPR013719 all species →	Domain	Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain	Interproscan
IPR038167 all species →	Homologous_superfamily	SSRP1 domain superfamily	Interproscan
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR024954 all species →	Domain	SSRP1, dimerization domain	Interproscan
IPR050454 all species →	Family	RTT106/SSRP1 Histone Chaperone/FACT Complex	Interproscan
IPR000969 all species →	Family	FACT complex subunit SSRP1/POB3	Interproscan
IPR035417 all species →	Domain	FACT complex subunit SSRP1/POB3, N-terminal PH domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45849 all species →	FACT COMPLEX SUBUNIT SSRP1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0031491 all species →	Molecular Function	nucleosome binding	Interproscan
GO:0035101 all species →	Cellular Component	FACT complex	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	Interproscan
GO:1902275 all species →	Biological Process	regulation of chromatin organization	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K09272	SSRP1, POB3; FACT complex subunit SSRP1/POB3	-	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 XP_032236023.2 across 48 RNA-seq samples of Nematostella vectensis. 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

44TPM > 0

16Conditions

41.7Max TPM

19.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	24.93	26.83
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	17.94	22.44
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	9.94	12.32
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	16.68	18.32
whole 6 week old aboral regenerate · regenerate uncut	3	3	12.44	14.40
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	21.96	26.81
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	20.71	22.93
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	33.80	41.66
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	25.06	30.68
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	21.10	24.83
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	15.22	15.61
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	30.41	37.57
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	30.12	31.46
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	20.09	33.08
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	10.88	17.26
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	4.90	14.71

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	26.83
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	24.46
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	23.50
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	22.44
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	17.68
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	13.71
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	12.32
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	8.92
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	8.57
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	18.32
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	18.09
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	13.63
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	14.40
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	12.30
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	10.62
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	26.81
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	23.52
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	15.55
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	22.93
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	20.72
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	18.48
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	41.66
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	31.28
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	28.47
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	30.68
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	24.01
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	20.50
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	24.83
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	19.37
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	19.10
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	15.61
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	15.49
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	14.55
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	37.57
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	27.78
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	25.89
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	31.46
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	31.20
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	27.72
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	33.08
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	27.17
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	17.26
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	15.38
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	14.71
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00

Source: CnidoSite RNA-seq expression matrices (NVECT_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.