H-InvDB x AHG DB
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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000035131 Accession number: BC010939 Created date: 26-Mar-2013 Last modified: 26-Mar-2013
Definition: Polyadenylate-binding protein 2.
 
 

Transcript original information
Accession number BC010939.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:13564 IMAGE:4333442
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PABPN1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PABPN1);
Sequence data provider Provider:MGC/NCI
Annotation project H-Invitational FLcDNA
Length of cDNA 1007[bp] (No. of exon:7)[A:257 T:151 G:350 C:249]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Skin, melanotic melanoma, high MDR.
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 978(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) TAGGAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0011537
Genomic location  G-integra Help Chromosome 14
Location 14q11.2
Position 23790675- 23794542
Strand +
Possible duplicated location(s) NA
Gene structure 7 exon(s)
Database links RefSeq NM_004050NM_004643NM_001199839NM_001199864
Ensembl ENST00000216727ENST00000250405ENST00000397276
Entrez Gene Entrez Gene ID:8106
KEGG GENES KEGG GENES(8106)
GeneCard GeneCardPABPN1*GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS G-integraG-integra cDNA-genome alignmentcDNA-genome alignment

Predicted CDS information
HIP ID HIP000021134
Predicted CDS 9..929;  306[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.756
Database links RefSeq NP_004634
UniProt F2Z5L8Q86U42
CCDS CCDS9592

Motif information
ORF

length(306),orf(9:929)
MAAAAAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGAPGGAGDYGNGL
ESEELEPEELLLEPEPEPEPEEEPPRPRAPPGAPGPGPGSGAPGSQEEEE
EPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMS
PPPGNAGPVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNR
VTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN
RPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGRARAT
SWYSPY*
a.a.
length
InterPro Name
length(106), motif(144:249) 106 IPR012677 Nucleotide-binding, alpha-beta plait [Domain]
length(78), motif(172:249) 78 IPR000504 RNA recognition motif domain [Domain]
length(73), motif(173:245) 73 IPR000504 RNA recognition motif domain [Domain]
length(70), motif(174:243) 70 IPR000504 RNA recognition motif domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000035131
H-Inv cluster ID Locus viewHIX0011537
Accession number BC010939.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Polyadenylate-binding protein 2.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_004634)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol PABPN1
HGNC aliases "poly(A)-binding protein, nuclear 1"
HGNC name poly(A) binding protein, nuclear 1
DDBJ PABPN1
UniProt NA
EC number NA
GGDB
(GlycoGene Database)
Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000021134
No. of interaction 10
Interaction partner(s) HIP000030181HIP000040935HIP000066953HIP000068162HIP000070686HIP000085571HIP000097977HIP000099536HIP000114160HIP000218351
BIND NA
DIP NA
MINT MINT-3297301;  MINT-7945693; 
HPRD 01242;  01574;  03183;  03422;  03685;  04210;  04340;  07601;  11934;  16246; 
IntAct EBI-932569;  EBI-3048562;  EBI-3046676;  EBI-2692183; 
Database links RefSeq NM_004050NM_004643NM_001199839NM_001199864
Ensembl ENST00000216727ENST00000250405ENST00000397276
Entrez Gene Entrez Gene ID:8106
KEGG GENES KEGG GENES(8106)
GeneCard GeneCardPABPN1*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Human curated
Notes NA
Related H-InvDB links Gene familyGene family;  Similarity Search ToolSimilarity Search Tool TACTTACT
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA

Gene ontology information
Molecular function nucleic acid binding (GO:0003676);  nucleotide binding (GO:0000166); 

Subcellular localization information  Last modified:26-Mar-2013
WoLF PSORT nuclear; 
Target P Not predicted
SOSUI soluble protein
TMHMM soluble protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:26-Mar-2013
Start End PDB_ID E-value Identity Coverage SCOP_ID
170 253 1wi8A 2e-16 25.0 84/104 d.58.7.1
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:26-Mar-2013
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene NA
Affymetrix
GeneChip
HG-Focus NA
HG-U133 201544_x_at; 
HG-U133A 201544_x_at; 
HG-U133A_2 201544_x_at; 
HG-U133B NA
HG-U133_Plus_2 201544_x_at; 
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 3529085;  3529088;  3529090;  3529094;  3840483;  3840484;  3981077;  4011934;  4011935; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 NA
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:26-Mar-2013
Disease relation Disease name: Oculopharyngeal muscular dystrophy (164300); 
Related information in OMIM OMIM ID:  602279;  Title: POLYADENYLATE-BINDING PROTEIN, NUCLEAR, 1
Co-localized orphan diseases NA
Disease related mutation MutationView:  602279
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(8106)
Disease Entrez Gene ID:(8106)
Substance Entrez Gene ID:(8106)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo ViewerLEGENDALEGENDA

Evolutionary information  Evola Help Last modified:26-Mar-2013
Relationship Species Accession number MGI Links
Orthology Mus sp. (Mouse) AK032172 G-integraG-integra
Orthology Bos sp. (Cow) BC133551 G-integraG-integra
Orthology Danio sp. (Zebrafish) BC154028 G-integraG-integra
Orthology Gallus sp. (Chicken) CR388838 G-integraG-integra
Orthology Macaca sp. (Macaque) ENSMMUT00000020685 G-integraG-integra
Orthology Oryzias sp. (Medaka) ENSORLT00000007713 G-integraG-integra
Orthology Pongo sp. (Orangutan) ENSPPYT00000006695 G-integraG-integra
Orthology Canis sp. (Dog) NM_001130437 G-integraG-integra
Orthology Pan sp. (Chimpanzee) XM_001162168 G-integraG-integra
Orthology Monodelphis sp. (Opossum) XM_001369290 G-integraG-integra
Orthology Equus sp. (Horse) XM_001493609 G-integraG-integra
Orthology Danio sp. (Zebrafish) XM_001923008 G-integraG-integra
Phylogenetic tree [View by ATV]
Neighbor-joining (phb) 
Related H-InvDB links EvolaEvoladN/dS (under constraction); 

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
43 .. 43 G/C rs104894466 + CDS Nonsynonymous[Gly12Ala]
482 .. 482 G/A rs2295126 + CDS Synonymous[Pro158Pro]
593 .. 593 T/G rs116983161 + CDS Nonsynonymous[Cys195Trp]
821 .. 821 C/T rs113160838 + CDS Synonymous[Thr271Thr]
 Microsatellite (Short Tandem Repeat, STR)
Location Variation Strand
11..31 (ggc)7 +
297..311 (gag)5 +
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer