Gene detail

Detailed information of XP_001640481.2 in Nematostella vectensis

Genomic Location: NC_064045.1:11888225...11896035
NR annotation: XP_001640481.2, pentatricopeptide repeat-containing protein 1, mitochondrial [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5520656

ATGGCTGCCTTGTTGAACATGAGTAAAGCAGCTTCAAAAGTTCTTTTGATTGGAAAAAACTCGCACTTGTTAACAAAGACGCAATATTTTTTTAGATATGAAAGTGTTATACATCAGAGGATGGGATATTCTAGTTTAAACCATGCGAGATTTGACAATTTGTACACACAACATGAGCCTATCCCTACAACTTCTCTACTACAACCACACAATGAAACTTCTACTTTCAATTCGCGTTTTAGCACGTGGAGAGGAAATAAGAAAAATCTATTTGCCAATTCTTCCAGCATTGATCCAGATGACCCAAAGAATGGTGCTTATGTCATTGAAGAAGGCAATGATGATGATGATTTTGATGATGATGATGTAGATAATGATGGCACAAAAGATTTTTTTAGAGAAAAAGACAAGCTTAAAAAGTTTACTAGTAAAAATATGTATAGTGAGAAAAGACCCAATCACAAAGCACAAAAGACTGTTGAGGGTAAAGTCAGATCGTCACGATATGTGTTCAAAGATCTACATGATGGGGAGGAGGATTTCCGATGGGTAAGGAGGCAGGGCCAAGTGGTGAGGTCAAGACGAAAAGGAGAGTGGTATGCTAATCAAATGTCAAGATTAGCCAATCAGAATCAGATTGAGAAAGCAGAAGAAATGCTACTTTCAATGAAACAGGAGGGGATCACCCAAAAGGCTGAAGTGATAAACATTCTGATAAGTGCTTATGCAAAGAAAGGAAATGCAAGAAAAGCGTTTCATCTTTATAATAACATCAAGAAAATGGGTCTGAAGGCTACCACACACACCTACACCAGTCTATTCAACTGCTGTGCCTTGTCTAACAATACCAAACTTACCAGAGCAAGCCTGGACAAGCTATGGGAGGAATTTCATCTCCGAGTCAACACAGAAGACATAAAACCCCATACCATCACCTACAACGCAGCTATCAAAGCATTTGCTCACTGCAGTACCCCTTTGAAAGCTTTTGAAGTCTATGAAGACATGCAAACCCATGGAGTGCAAGTTGATGGTTACACATCGGCAGCCCTGCTGGCAGCCTGTGCGGCAATGGGTAGGGGGGGACCAGCCAAGGCCATGTTAGTGCTGGAGGAGATGAAGGAGCAAGGAGTGAAATTGGATATTTATGTGTTCAATTTAGTTCTCAAAGTTATAAGGGATGCGAAATTTGATCACTTGAAGAAAAATCCTGAGAAGGCATCTATCACATTTGAAAAACAGCATAAGGATAGTATTCTTAATGGTTCTTTTGGTGGAGATATTCAGAATAATACTGGGACTTTAGGAGATGATCACAGAGGTTTGGCAAGGTTAGATGTTAAACAAAACACCAAGGCTGAACAATGCTTTAAGGATTTGATTCCTGCTGTTCAAGAAGTTCCTAAAAATTCTGTGTTTCAAACAAAGGGTAAGACATCTCCCTTGGGGGTCAACCTCTTTGCTGGAGTTGAGAGTTTTGTTCAGTTGATGGCTGTCAATGAAGTGAAGCCAGACATTCGGACATTCCATTTGATGCTTCAACTAGCAAACGATGGTGTAGAACAGGAGAATAACCTTCTGCAGGTGATGGAGAGGTGTGGAATTAGCCCTGATATGGCAATGCTGAACACTCTTGTGAGGAGAAGGGCTCGAAAAGGCGATGTCACTACCGCTAAGGAATATATAGAAAACTTCAGCATCCGGTATAGCCTATCTGCTGATGAGAGAACCTATGTGATTTTGGCAAGTGGGTGTAGAACCACTAAAGATGGACTCTGGCTTCTTCAAGAAATGAAGGATAGAGGACTTCAGTCTAGCCAAGCTGTGTACATGAAGTTGTTATTTTGTGCATCAAGAAGTCACAACTACCCACACATGATAACTTTGCTTAAGGTAATCAAAAAAGAGGGCATACAGCCACTGGATGGAATCCTGTCATTAATGGATAAGATTTGTTATCACACACAGAAGGGAGAATCAAAAAGGGATGTTGAGACGAATAAAAAGCTGAAAAGGAAAGCAAAATTCTTACAGACACAGCGAGCAAGCCTCCTTGAGCACTACTCTCACTGGAGACAAGGACTGATACCCAACAATGATGTGGATCTAGATGACACAGAAGAGAAAAATTATGATCATTTGTAA

Transcript

rna-XM_001640431.3

ACTGCTTGTAAAtgcttttttaaaagctgaAATACAACATTTTACGGGATGCCTGtgctttttgttgctattACGAACAGCCAGTCAGCGGGTACACAACGAGACTCAGACTCAAGATGGCTGCCTTGTTGAACATGAGTAAAGCAGCTTCAAAAGTTCTTTTGATTGGAAAAAACTCGCACTTGTTAACAAAgacgcaatatttttttagatatgaAAGTGTTATACATCAGAGGATGGGATATTCTAGTTTAAACCATGCGAGATTTGACAATTTGTACACACAACATGAGCCTATCCCTACAACTTCTCTACTACAACCACACAATGAAACTTCTACTTTCAATTCGCGTTTTAGCACGTGGAgaggaaataagaaaaatctATTTGCCAATTCTTCCAGCATTGATCCAGATGACCCAAAGAATGGTGCTTATGTCATTGAAGAaggcaatgatgatgatgattttgatgatgatgatgtagatAATGATGGcacaaaagatttttttagagaaaaagACAAGCTTAAAAAGTTTACTAGTAAAAATATGTATAGTGAGAAAAGACCCAATCACAAAGCACAAAAGACTGTTGAGGGTAAAGTCAGATCGTCACGATATGTGTTCAAAGATCTACATGATGGGGAGGAGGATTTCCGATGGGTAAGGAGGCAGGGCCAAGTGGTGAGGTCAAGACGAAAAGGAGAGTGGTATGCtaatcaaatgtcaagattagccaatcagaatcagATTgagaaagcagaagaaatgcTACTTTCAATGAAACAGGAGGGGATCACCCAAAAGGCTGAAGTGATAAACATTCTGATAAGTGCTTATGCAAAGAAAGGAAATGCAAGAAAAGCGTTTCATCTTTATAATAACATCAAGAAAATGGGTCTGAAGGCTACCACACACACCTACACCAGTCTATTCAACTGCTGTGCCTTGTCTAACAATACCAAACTTACCAGAGCAAGCCTGGACAAGCTATGGGAGGAATTTCATCTCCGAGTCAACACAGAAGACATAAAACCCCATACCATCACCTACAACGCAGCTATCAAAGCATTTGCTCACTGCAGTACCCCTTTGAAAGCTTTTGAAGTCTATGAAGACATGCAAACCCATGGAGTGCAAGTTGATGGTTACACATCGGCAGCCCTGCTGGCAGCCTGTGCGGCAATGGGTAGGGGGGGACCAGCCAAGGCCATGTTAGTGCTGGAGGAGATGAAGGAGCAAGGAGTGAAATTGGATATTTATGTGTTCAATTTAGTTCTCAAAGTTATAAGGGATGCGAAATTTGATCACTTGAAGAAAAATCCTGAGAAGGCATCTATCACATTTGAAAAACAGCATAAGGATAGTATTCTTAATGGTTCTTTTGGTGGAGATATTCAGAATAATACTGGGACTTTAGGAGATGATCACAGAGGTTTGGCAAGGTTAGATGTTAAACAAAACACCAAGGCTGAACAATGCTTTAAGGATTTGATTCCTGCTGTTCAAGAAGTTCCTAAAAATTCTGTGTTTCAAACAAAGGGTAAGACATCTCCCTTGGGGGTCAACCTCTTTGCTGGAGTTGAGAGTTTTGTTCAGTTGATGGCTGTCAATGAAGTGAAGCCAGACATTCGGACATTCCATTTGATGCTTCAACTAGCAAACGATGGTGTAGAACAGGAGAATAACCTTCTGCAGGTGATGGAGAGGTGTGGAATTAGCCCTGATATGGCAATGCTGAACACTCTTGTGAGGAGAAGGGCTCGAAAAGGCGATGTCACTACCGCTAAGGAATATATAGAAAACTTCAGCATCCGGTATAGCCTATCTGCTGATGAGAGAACCTATGTGATTTTGGCAAGTGGGTGTAGAACCACTAAAGATGGACTCTGGCTTCTTCAAGAAATGAAGGATAGAGGACTTCAGTCTAGCCAAGCTGTGTACATGAAGTTGTTATTTTGTGCATCAAGAAGTCACAACTACCCACACATGATAACTTTGCTTAAGGTAATCAAAAAAGAGGGCATACAGCCACTGGATGGAATCCTGTCATTAATGGATAAGATTTGTTATCACACACAGAAGGGAGAATCAAAAAGGGATGTTGAGACGAATAAAAAGCTGAAAAGGAAAGCAAAATTCTTACAGACACAGCGAGCAAGCCTCCTTGAGCACTACTCTCACTGGAGACAAGGACTGATACCCAACAATGATGTGGATCTAGATGACACAGAAGAGAAAAATTATGATCATTTGTAAGCAAACCCAAGGCCTGGCTACTTTTAATCAATCAGGGTCCAGTTCCTGAAAGGCAGAATAGGTTATTCATTGGATAAATGTTGTCCTTGACTAATCAAATGACTAGAATAGCCAAGTGATCCCTGCAATAAACCTATTCTGCCTTTCAGGAACTGAGCCCTTGATTAAAAGGACCCGAATTAATATTCCCCAGTGAGTTATGCAACTATTCCTAATCAAATGACAGTGTAAGTGAAATAAAATACATCTTATActctatattttatttatttaaaaaaataaaattcatatATAACTATA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A2VD13	Pentatricopeptide repeat-containing protein 1, mitochondrial OS=Rattus norvegicus OX=10116 GN=Ptcd1 PE=2 SV=1
O75127	Pentatricopeptide repeat-containing protein 1, mitochondrial OS=Homo sapiens OX=9606 GN=PTCD1 PE=1 SV=2
Q8C2E4	Pentatricopeptide repeat-containing protein 1, mitochondrial OS=Mus musculus OX=10090 GN=Ptcd1 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009404 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13812 all species →	PPR_3	Pentatricopeptide repeat domain	Repeat	Interproscan
PF01535 all species →	PPR	PPR repeat	Repeat	Interproscan
PF13041 all species →	PPR_2	PPR repeat family	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002885 all species →	Repeat	Pentatricopeptide repeat	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47936 all species →	PPR_LONG DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0009507 all species →	Cellular Component	chloroplast	Interproscan
GO:0010019 all species →	Biological Process	chloroplast-nucleus signaling pathway	Interproscan
GO:0031930 all species →	Biological Process	mitochondria-nucleus signaling pathway	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_001640481.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_001640481.2 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

35TPM > 0

16Conditions

5.2Max TPM

2.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	1	1.74	5.21
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	3.69	4.18
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	4.09	4.78
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	3.90	4.09
whole 6 week old aboral regenerate · regenerate uncut	3	3	3.64	3.71
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	1.29	3.88
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	3.03	4.98
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	3.80	5.08
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	2.34	3.87
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	2.47	3.86
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	3.64	3.86
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	2.91	4.54
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	4.06	4.88
whole 6 week old aboral regenerate · regenerate 48hpa	3	1	1.63	4.90
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	2.75	4.27
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	1.19	3.57

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	5.21
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
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	4.18
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	3.96
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.92
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	4.78
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.78
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.70
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	4.09
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.85
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.77
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.71
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.67
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.53
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	3.88
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	4.98
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	4.11
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	5.08
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	4.34
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	1.97
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	3.87
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	3.16
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	3.86
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	3.55
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	3.86
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	3.73
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	3.33
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	4.54
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	4.20
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	4.88
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	4.30
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	3.01
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	4.90
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
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	4.27
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	3.99
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	3.57
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.