WaspAtlas A Nasonia vitripennis gene database





Cold shock domain-containing protein E1
Uncharacterized LOC100123206


Gene summary

Full name
Cold shock domain-containing protein E1
Type
gene
Description
uncharacterized LOC100123206
Aliases
LOC100123206, uncharacterized LOC100123206, NV10220, Unr, Cold shock domain-containing protein E1

NCBI (Latest) locus
LOC100123206
(NC_015867.2:27313068-27320342:-)
NCBI (Nvit_2.0 archived) locus
LOC100123206
(NC_015867.1:45416405-45423657:-)
EvidentialGene dataset locus
Nasvi2EG000436
(SCAFFOLD1:3167336-3173982:-)
Official gene set v1.2 locus
NV10220
(1:27313674-27318307:-)


Gene ontology annotation

78 associated GO terms
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GO:0003674 (molecular_function)
GO:0003676 (nucleic acid binding)
GO:0003677 (DNA binding)
GO:0003723 (RNA binding)
GO:0003729 (mRNA binding)
GO:0003730 (mRNA 3'-UTR binding)
GO:0005488 (binding)
GO:0005515 (protein binding)
GO:0005575 (cellular_component)
GO:0005622 (intracellular)
GO:0005623 (cell)
GO:0005737 (cytoplasm)
GO:0006355 (regulation of transcription, DNA-templated)
GO:0006417 (regulation of translation)
GO:0007154 (cell communication)
GO:0007267 (cell-cell signaling)
GO:0007549 (dosage compensation)
GO:0008150 (biological_process)
GO:0009047 (dosage compensation by hyperactivation of X chromosome)
GO:0009889 (regulation of biosynthetic process)
GO:0009890 (negative regulation of biosynthetic process)
GO:0009892 (negative regulation of metabolic process)
GO:0009987 (cellular process)
GO:0010468 (regulation of gene expression)
GO:0010556 (regulation of macromolecule biosynthetic process)
GO:0010558 (negative regulation of macromolecule biosynthetic process)
GO:0010605 (negative regulation of macromolecule metabolic process)
GO:0010608 (posttranscriptional regulation of gene expression)
GO:0010629 (negative regulation of gene expression)
GO:0016043 (cellular component organization)
GO:0017148 (negative regulation of translation)
GO:0019219 (regulation of nucleobase-containing compound metabolic process)
GO:0019222 (regulation of metabolic process)
GO:0022607 (cellular component assembly)
GO:0023052 (signaling)
GO:0030154 (cell differentiation)
GO:0031323 (regulation of cellular metabolic process)
GO:0031324 (negative regulation of cellular metabolic process)
GO:0031326 (regulation of cellular biosynthetic process)
GO:0031327 (negative regulation of cellular biosynthetic process)
GO:0032268 (regulation of cellular protein metabolic process)
GO:0032269 (negative regulation of cellular protein metabolic process)
GO:0032502 (developmental process)
GO:0034622 (cellular macromolecular complex assembly)
GO:0040029 (regulation of gene expression, epigenetic)
GO:0042714 (dosage compensation complex assembly)
GO:0043933 (macromolecular complex subunit organization)
GO:0044085 (cellular component biogenesis)
GO:0044424 (intracellular part)
GO:0044464 (cell part)
GO:0044699 (single-organism process)
GO:0044700 (single organism signaling)
GO:0044763 (single-organism cellular process)
GO:0044767 (single-organism developmental process)
GO:0044822 (poly(A) RNA binding)
GO:0045165 (cell fate commitment)
GO:0045168 (cell-cell signaling involved in cell fate commitment)
GO:0046331 (lateral inhibition)
GO:0048519 (negative regulation of biological process)
GO:0048523 (negative regulation of cellular process)
GO:0048869 (cellular developmental process)
GO:0050789 (regulation of biological process)
GO:0050794 (regulation of cellular process)
GO:0051171 (regulation of nitrogen compound metabolic process)
GO:0051246 (regulation of protein metabolic process)
GO:0051248 (negative regulation of protein metabolic process)
GO:0051252 (regulation of RNA metabolic process)
GO:0060255 (regulation of macromolecule metabolic process)
GO:0065003 (macromolecular complex assembly)
GO:0065007 (biological regulation)
GO:0071840 (cellular component organization or biogenesis)
GO:0080090 (regulation of primary metabolic process)
GO:0097159 (organic cyclic compound binding)
GO:1901363 (heterocyclic compound binding)
GO:1903506 (regulation of nucleic acid-templated transcription)
GO:2000112 (regulation of cellular macromolecule biosynthetic process)
GO:2000113 (negative regulation of cellular macromolecule biosynthetic process)
GO:2001141 (regulation of RNA biosynthetic process)

Orthologs in other species

Show/hide

AAEL010018 (Aedes aegypti)
ACEP25129 (Atta cephlotes)
Aqu1.203012 (Amphimedon queenslandica)
Aqu1.210254 (Amphimedon queenslandica)
BGIBMGA000629 (Bombyx mori)
ENSG00000009307 (Homo sapiens)
ENSMUSG00000068823 (Mus musculus)
FBgn0263352 (Drosophila melanogaster)
GB11497 (Apis mellifera)
GB44291 (Apis mellifera)
SINV23787 (Solenopsis invicta)
TC002472 (Tribolium castaneum)

▼  Transcripts

Dataset


Annotated transcripts: 1

Annotated transcripts: 2

Annotated transcripts: 1

Annotated transcripts: 2

XM_008217188.1

Location
NC_015867.2:27313068-27320342:-
No exons
12
Length
5608 bp




XM_001606768.3

Location
NC_015867.2:27313068-27320342:-
No exons
11
Length
5707 bp




XM_001606768.2

Location
NC_015867.1:45416405-45423657:-
No exons
11
Length
5685 bp




Nasvi2EG000436t1

Location
SCAFFOLD1:3167336-3171969:-
No exons
10
Length
3930 bp




Nasvi2EG000436t2

Location
SCAFFOLD1:3168432-3173982:-
No exons
11
Length
3983 bp




NV10220-RA

Location
1:27313674-27318307:-
No exons
10
Length
3930 bp




▼  Protein annotation

Dataset


Predicted PFAM domains

PF00313.17 ('Cold-shock' DNA-binding domain)
PF12901.2 (SUZ-C motif)

Predicted PFAM domains

PF00313.17 ('Cold-shock' DNA-binding domain)
PF12901.2 (SUZ-C motif)

Predicted PFAM domains

PF00313.17 ('Cold-shock' DNA-binding domain)
PF12901.2 (SUZ-C motif)

Predicted PFAM domains

PF00313.17 ('Cold-shock' DNA-binding domain)
PF12901.2 (SUZ-C motif)

▼  Expression data

RNA-seq expression data

Expression data is based on NCBI annotation Nvit v2.1. Enrichment values are given relative to whole-body RNA-seq samples of the same sex (Male whole-body (1) for males, and Female whole-body (1) for females).

Each row represents a different set of RNA-seq samples. Full information about each sample set can be found on the downloads page.

Expression data for transcript XM_008217188.1

Expression
(FPKM ± Stddev)		 Presence
(No. samples)		 Relative
enrichment
Female whole-body (1) 7.2586 ± 1.6714 3 of 3
Female whole-body (2) 3.5011 ± 3.4995 2 of 2 0.48
Female whole-body (3) 7.9516 1 of 1 1.10
Female whole-body (4) 17.0721 ± 0.7212 2 of 2 2.35
Female head (1) 1.9293 ± 1.0563 11 of 12 0.27
Female head (2) 0.4836 ± 0.4964 5 of 6 0.07
Male whole-body (1) 14.5783 ± 4.5864 3 of 3
Male head (1) 1.8338 ± 1.0804 12 of 12 0.13
Male testis (1) 8.4896 1 of 1 0.58
Male testis (2) 8.7289 1 of 1 0.60

Expression data for transcript XM_001606768.3

Expression
(FPKM ± Stddev)		 Presence
(No. samples)		 Relative
enrichment
Female whole-body (1) 70.9154 ± 6.6257 3 of 3
Female whole-body (2) 48.9453 ± 5.9527 2 of 2 0.69
Female whole-body (3) 65.5156 1 of 1 0.92
Female whole-body (4) 40.2486 ± 0.4478 2 of 2 0.57
Female head (1) 43.9688 ± 1.6421 12 of 12 0.62
Female head (2) 61.4735 ± 2.0567 6 of 6 0.87
Male whole-body (1) 37.1747 ± 12.3862 3 of 3
Male head (1) 37.8547 ± 2.3857 12 of 12 1.02
Male testis (1) 127.2080 1 of 1 3.42
Male testis (2) 142.7380 1 of 1 3.84

Tiling microarray developmental expression data

Genome-wide tiling microarray data was generated by Wang et al. in 2013 and can be accessed here:
Function and evolution of DNA methylation in Nasonia vitripennis

Expression data for Nasvi2EG000436

Expression (log2)
Female early embryo 13.2008
Female late embryo 12.1054
Female larva 12.6590
Female pupa 13.4522
Female adult 13.0329
Ovary 13.3043


▼  Studies

RRBS diapause methylation data (Pegoraro & Bafna et al, 2015) show/hide

Study name
DNA methylation changes induced by long and short photoperiods in Nasonia
Annotation
NCBI (archived) Nvit_2.0
Gene
LOC100123206
Summary:

Long day coverage
7 CpG sites covered, 0 methylated, 7 non-methylated
Short day coverage
7 CpG sites covered, 0 methylated, 7 non-methylated

No differentially methylated CpG sites detected for this gene
Download full raw data for this gene

Upstream conserved non-coding elements (Davies et al, 2015) show/hide

Study name
Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals
Annotation
Official gene set v1.2 (Ensembl)

NV10220 upstream conserved non-coding elements diagram


NV10220-1 information
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Sequence comparison

Raw FASTA sequences
Download
GC content
0.53
ATG O/E
2.36
Conserved in
Nasonia vitripennis (NV10220)
Heliconius melpomene (HMEL010553)
Danaus plexippus (KGM_15374)
Bombyx mori (BGIBMGA000629)

RNA structure conserved?
p = 0.131 (Very unlikely)
RNA structure plots
Show/hide
Nasonia vitripennis
Heliconius melpomene
Danaus plexippus
Bombyx mori


Images are coloured by nucleotide conservation from 0 (weak) to 1.0 (strong)


NV10220-2 information
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Sequence comparison

Raw FASTA sequences
Download
GC content
0.33
ATG O/E
0.43
Conserved in
Nasonia vitripennis (NV10220)
Solenopsis invicta (SINV23787)
Dendroctonus ponderosae (YQE_12424)
Atta cephalotes (ACEP25129)
Tribolium castaneum (TCOGS2:TC002472)
Apis mellifera (GB11497)
Heliconius melpomene (HMEL010553)

RNA structure conserved?
p = 0.256 (Very unlikely)
RNA structure plots
Show/hide
Nasonia vitripennis
Solenopsis invicta
Dendroctonus ponderosae
Atta cephalotes
Tribolium castaneum
Apis mellifera
Heliconius melpomene


Images are coloured by nucleotide conservation from 0 (weak) to 1.0 (strong)


NV10220-3 information
Show/hide

Sequence comparison

Raw FASTA sequences
Download
GC content
0.32
ATG O/E
0.28
Conserved in
Nasonia vitripennis (NV10220)
Solenopsis invicta (SINV23787)
Atta cephalotes (ACEP25129)
Apis mellifera (GB11497)

RNA structure conserved?
p = 0.309 (Very unlikely)
RNA structure plots
Show/hide
Nasonia vitripennis
Solenopsis invicta
Atta cephalotes
Apis mellifera


Images are coloured by nucleotide conservation from 0 (weak) to 1.0 (strong)