Gene detail

Detailed information of XP_048587253.1 in Nematostella vectensis

Genomic Location: NC_064041.1:3612189...3622200
NR annotation: XP_048587253.1, LOW QUALITY PROTEIN: tetratricopeptide repeat protein 16 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5505871

ATGTCAAACTCTAGGAGTAAGAAGTCAACTAATGGAGATGAGAGTGTACAATCAGGGGAAAATGACTTGGAAAATAATCGCGCGTTAGTCCCTTTTAAAGAAAAAGACTCCGGAACAACGGCTGATTCTTCAGGGAACGAAACAGACGATAGCGAGGTGAACGAGCTCAAAGCGCAGGTTGCTGTGGAAAGAAGGCATCGGAGGAAAACTATTGTAAACTCTTTTCGTCTAGCAGAACTCATACCTACTCCGAACACTCCTTATTCAAGCTACAGGCGAAAGTCGATCGCGCTTACAGTACAAAGTGTTATTGACTCGAAAGCTAAGTATCATTTTATTGAAGGAATCACAAAATCAGAAGATGGCCAGCATTACAAAGCAATTGCATGCTTCAATAAAGCGATCTCCTTGAAACCTGAATTGATAAAATACTACACAGCTAGAGGGGAATCCTTCTTGCAAATATGTGACTTTCAGTCCGCCATATTGAACTTTAAAAAGGCCTGTATATTGGATCCTGAAAATGATGAATACTATTCAAGATTAGCATTTATATACTTCTTTCAAGGACAATGTTTATTTGATGAAAAACTTTATAAGGAAGCTTTGGAATCATTTTCTCGAGCCGCAGAAATGAAGCCTGAGGTCATTGGGTACCATACAAGAAGTGTGGCTTGCCTGTCAGCACTTCAGAGACATGGGGAATGTCTGGCTCTAGTCAACAAAAGGCTAGAGGAAGAGAGTACCAATACGGATCTCTACATTATGAGGGCGCGGCTACATGAGCTCTTTAGGAATTCTACCTTGTGTTATTATGATGTCAAAGACGCCTTGGTACTATCTCCAGATAATGAGGAGGCCAAAACTCTCATGAACTCTTTGCATAAAAGAGCCAATGATAGTAAGCTACAGGCTGAACAACTGTTCCTAGTAGGCAAAGTAAAAGAAGCGTTAACAAAAATCTCCATAGCGATAGAGACCAACCCTTCAATACCAGAGTATCACGTATTCAGGGGTGCCCTTCATCGCAAACACGCGGATTTCAATGCTGCCATAGATGACTTTCTCCTCGCGATGGACAAGACCGACCACGACGAGTCCCATCCCACTTATAAACACGCTCAGCGACAACTTCTCCTGTCCTATAACGACTTTGCTGTCGAGTGTTTCGGAAAGGGTTATTATGACGAGGCCATAGTGCTGTTGAACAAGGCCGTCCAGGGAGAGAAGAACGAAAAAGGGCTGTACATCAACAGGGGAGATTGCTTCTTTCGCGCTAACGAGCTTCACTTTGCTCTGGCCGACTATCAGCAAGCCTTGGAGATGGACCCAGCAAGCCAGGCTATCCGGTCACGCCTGTCAATCGTGTTTAACGAGTTTGGGATTCTGGAATACTACGACCGTCACTACCTAGAGTCAATAGATTACCTAACCACGGCCATCAGCTACAACCCTCGCATCGGGCCGTATTACCTGTCCCGCGCAAGGGCGAGGTACATGATAGAGGACAGTGACGGCGCCCGTGAAGACGTCCTCAAATGCCTGTATCTGGAACCCGACAGCAAGGAAGTGGTGTCGATCTTCTCAAGGCTCTTCCCAGGAAGAAGTATTAGTGACGTCACGAAAGGCCAGCTGGGGCTGTCAGCCGCGCGTGCTGTCGAGGCTCACATACGGGATACCATAGGGAACGCGTTGCCAATAGTTACAAGCTCCATGAAAGTGTCCTCGTCCCAGTTCTCCGGGAGGTTTATTCTCCCGCCCATCCGGGACTCTGTGCTGCCTGAGATACGCGCGTGTATGGAGCAAGACTTCCACGTGAACATTATCAAGAGCAAGCTACAGGCTACCAGGGTCGTCAAGAAAGCATTTAACGCTCGACAGAACCTATCTTATAAGGGCCCTCGTGTGAGCGCCCCTCGTGCCCAGGCCCCGCTGTCAGCTATCAAGACGTTTAAATGGGAGACTAGTGTTACTCAAAGGGCTCTGCCCAAAACAATCGCGAGCGAGCGAAAACCACTGACATACCCCGCTTAG

Transcript

rna-XM_048731296.1

GGTATAGCTGGTATCTTAGCAACGTTAAAAACATGGCGGGTTGTTGTCAAATGGAGTCAAATCACTATAATTTACCAATTATTCAGAGCTAAGGTTCGAGTAAATCGTACCTAATGTCAAACTCTAGGAGTAAGAAGTCAACTAATGGAGATGAGAGTGTACAATCAGGGGAAAATGACTTGGAAAATAATCGCGCGTTAGTcccttttaaagaaaaagacTCCGGAACAACGGCTGATTCTTCAGGGAACGAAACAGACGATAGCGAGGTGAACGAGCTCAAAGCGCAGGTTGCTGTGGAAAGAAGGCATCGGAGGAAAACTATTGTAAACTCTTTTCGTCTAGCAGAACTCATACCTACTCCGAACACTCCTTATTCAAGCTACAGGCGAAAGTCGATCGCGCTTACAGTACAAAGTGTTATTGACTCGAAAGCTAAGTATCATTTTATTGAAGGAATCACAAAATCAGAAGATGGCCAGCATTACAAAGCAATTGCATGCTTCAATAAAGCGATCTCCTTGAAACCTGAATTGATAAAATACTACACAGCTAGAGGGGAATCCTTCTTGCAAATATGTGACTTTCAGTCCGCCATATTGAACTTTAAAAAGGCCTGTATATTGGATCCTGAAAATGATGAATACTATTCAAGATTAGCATTTATATACTTCTTTCAAGGACAATGTTTATTTGATGAAAAACTTTATAAGGAAGCTTTGGAATCATTTTCTCGAGCCGCAGAAATGAAGCCTGAGGTCATTGGGTACCATACAAGAAGTGTGGCTTGCCTGTCAGCACTTCAGAGACATGGGGAATGTCTGGCTCTAGTCAACAAAAGGCTAGAGGAAGAGAGTACCAATACGGATCTCTACATTATGAGGGCGCGGCTACATGAGCTCTTTAGGAATTCTACCTTGTGTTATTATGATGTCAAAGACGCCTTGGTACTATCTCCAGATAATGAGGAGGCCAAAACTCTCATGAACTCTTTGCATAAAAGAGCCAATGATAGTAAGCTACAGGCTGAACAACTGTTCCTAGTAGGCAAAGTAAAAGAAGCGTTAACAAAAATCTCCATAGCGATAGAGACCAACCCTTCAATACCAGAGTATCACGTATTCAGGGGTGCCCTTCATCGCAAACACGCGGATTTCAATGCTGCCATAGATGACTTTCTCCTCGCGATGGACAAGACCGACCACGACGAGTCCCATCCCACTTATAAACACGCTCAGCGACAACTTCTCCTGTCCTATAACGACTTTGCTGTCGAGTGTTTCGGAAAGGGTTATTATGACGAGGCCATAGTGCTGTTGAACAAGGCCGTCCAGGGAGAGAAGAACGAAAAAGGGCTGTACATCAACAGGGGAGATTGCTTCTTTCGCGCTAACGAGCTTCACTTTGCTCTGGCCGACTATCAGCAAGCCTTGGAGATGGACCCAGCAAGCCAGGCTATCCGGTCACGCCTGTCAATCGTGTTTAACGAGTTTGGGATTCTGGAATACTACGACCGTCACTACCTAGAGTCAATAGATTACCTAACCACGGCCATCAGCTACAACCCTCGCATCGGGCCGTATTACCTGTCCCGCGCAAGGGCGAGGTACATGATAGAGGACAGTGACGGCGCCCGTGAAGACGTCCTCAAATGCCTGTATCTGGAACCCGACAGCAAGGAAGTGGTGTCGATCTTCTCAAGGCTCTTCCCAGGAAGAAGTATTAGTGACGTCACGAAAGGCCAGCTGGGGCTGTCAGCCGCGCGTGCTGTCGAGGCTCACATACGGGATACCATAGGGAACGCGTTGCCAATAGTTACAAGCTCCATGAAAGTGTCCTCGTCCCAGTTCTCCGGGAGGTTTATTCTCCCGCCCATCCGGGACTCTGTGCTGCCTGAGATACGCGCGTGTATGGAGCAAGACTTCCACGTGAACATTATCAAGAGCAAGCTACAGGCTACCAGGGTCGTCAAGAAAGCATTTAACGCTCGACAGAACCTATCTTATAAGGGCCCTCGTGTGAGCGCCCCTCGTGCCCAGGCCCCGCTGTCAGCTATCAAGACGTTTAAATGGGAGACTAGTGTTACTCAAAGGGCTCTGCCCAAAACAATCGCGAGCGAGCGAAAACCACTGACATACCCCGCTTAGACACACCATCaaattttatagaataaaatatttatattcttA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q95LZ5	Tetratricopeptide repeat protein 16 OS=Macaca fascicularis OX=9541 GN=TTC16 PE=2 SV=1
Q8NEE8	Tetratricopeptide repeat protein 16 OS=Homo sapiens OX=9606 GN=TTC16 PE=1 SV=2
Q8C1F5	Tetratricopeptide repeat protein 16 OS=Mus musculus OX=10090 GN=Ttc16 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007692 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13181 all species →	TPR_8	Tetratricopeptide repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR019734 all species →	Repeat	Tetratricopeptide repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45153 all species →	TETRATRICOPEPTIDE REPEAT PROTEIN 16	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	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

No KEGG orthology assignment for XP_048587253.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_048587253.1 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

35TPM > 0

16Conditions

11.5Max TPM

3.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	1	0.97	2.90
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	2.19	3.16
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	2.54	3.21
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	7.66	7.97
whole 6 week old aboral regenerate · regenerate uncut	3	3	5.75	11.54
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	1.52	4.56
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	1.99	3.05
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	3.45	6.54
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	2.92	4.93
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	4.89	11.22
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	4.03	6.06
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	4.53	7.23
whole 6 week old aboral regenerate · regenerate 60hpa	3	2	1.90	2.86
whole 6 week old aboral regenerate · regenerate 48hpa	3	1	1.20	3.59
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	2.09	3.98
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	1.90	5.71

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	2.90
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	3.16
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	1.95
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	1.46
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.21
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	2.61
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	1.81
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	7.97
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	7.86
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	7.15
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	11.54
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	2.95
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	2.77
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	4.56
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	3.05
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	2.91
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	6.54
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	2.07
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	1.74
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	4.93
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	3.85
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	11.22
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	3.45
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	6.06
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	3.06
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	2.98
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	7.23
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	3.39
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	2.97
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	2.86
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	2.84
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	0.00
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	3.59
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320871	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	3.98
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	2.28
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	5.71
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.