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H-Invitational ID: HIT000422812 Accession number: AK290015 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: R3H domain-containing protein 1;
 
 

Transcript original information
Accession number AK290015.1
CAGE tag ID NA
EST ID NA
Clone Number BRHIP3027701
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (R3HDM1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (R3HDM1);
Sequence data provider NA
Annotation project NA
Length of cDNA 3673[bp] (No. of exon:26)[A:1125 T:850 G:736 C:962]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type hippocampus
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGGAG;  TAGCAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0002476
Genomic location  G-integra Help Chromosome 2
Location 2q21.3
Position 136344007- 136481913
Strand +
Possible duplicated location(s) NA
Gene structure 26 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:23518
KEGG GENES KEGG GENES(23518)
GeneCard GeneCardR3HDM1*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 HIP000191833
Predicted CDS 320..3622;  1100[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.724

Motif information
ORF

length(1100),orf(320:3622)
MRMSDTVTVKDETATMKDLEAEVKDTTRVENLIKSENYGKILVEKNEHCI
ENNIDLQRPLQSFGQTGKRSKSSSKLKLVRSLAVCEESPPPPAPEISQEN
QEKIQIQLTQSFEKEEKPSKDEAEEEKASDKLPRKMLSRDSSQEYTDSTG
IDLHEFLVNTLKNNPRDRMMLLKLEQEILDFIGNNESPRKKFPPMTSYHR
MLLHRVAAYFGLDHNVDQSGKSVIVNKTSNTRIPDQKFNEHIKDDKGEDF
QKRYILKRDNSSFDKDDNQMRIRLKDDRRSKSIEEREEEYQRARDRIFSQ
DSLCSQENYIIDKRLQDEDASSTQQRRQIFRVNKDASGRSTNSHQSSTEN
ELKYSEPRPWSSTDSDSSLRNLKPAVTKASSFSGISVLTRGDSSGSSKSI
GRLSKTGSESSGSVGSSTGSLSHIQQPLPGTALSQSSHGAPVVYPTVSTH
SSLSFDGGLNGQVASPSTSFFLLPLEAAGIPPGSILINPQTGQPFINPDG
SPVVYNPPMTQQPVRSQVPGPPQPPLPAPPQQPAANHIFSQQDNLGSQFS
HMSLARQPSADGSDPHAAMFQSTVVLQSPQQSGYIMTAAPPPHPPPPPPP
PPPPPPLPPGQPVPTAGYPASGHPVSQPVLQQQGYIQQPSPQMPACYCAP
GHYHSSQPQYRPVPSVHYNSHLNQPLPQPAQQTGYQVIPNQQQNYQGIVG
VQQPQSQSLVSGQPNSIGNQIQGVVIPYTSVPTYQVSLPQGSQGIPHQTY
QQPVMFPNQSNQGSMPTTGMPVYYSVIPPGQQNNLSSSVGYLQHPGSEQV
QFPRTTSPCSSQQLQGHQCTAGPPPPPGGGMVMMQLSVPNNPQSCAHSPP
QWKQNKYYCDHQRGQKCVEFSSVDNIVQHSPQLSSPIISPAQSPAPAQLS
TLRTVRPSGPPLSIMPQFSRPFVPGQGDSRYPLLGQPLQYNPPAVLHGHI
PNQQGQPGSRHGNRGRRQAKKAASTDLGAGETVVGKVLEITELPDGITRM
...
a.a.
length
InterPro Name
length(122), motif(140:261) 122 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(78), motif(151:228) 78 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(64), motif(168:231) 64 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(61), motif(168:228) 61 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(64), motif(171:234) 64 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(71), motif(232:302) 71 IPR024771 SUZ domain [Domain]
length(51), motif(251:301) 51 IPR024771 SUZ domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000422812
H-Inv cluster ID Locus viewHIX0002476
Accession number AK290015.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition R3H domain-containing protein 1;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q15032)  [Identity/coverage = 99.636%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 7584026151441861548933418669648196903322006823121406692ALL
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 R3HDM1
HGNC aliases "R3H domain (binds single-stranded nucleic acids) containing"
HGNC name R3H domain containing 1
DDBJ NA
UniProt R3HDM1
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 HIP000191833
No. of interaction 3
Interaction partner(s) HIP000034631HIP000053050HIP000071861
BIND NA
DIP 111932E; 
MINT MINT-2871037; 
HPRD 01921;  03333; 
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:23518
KEGG GENES KEGG GENES(23518)
GeneCard GeneCardR3HDM1*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Auto-annotated
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); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT nuclear;  cytosol; 
Target P Other
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:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
141 261 1whrA 1e-32 75.2 121/124 d.68.7.1
Related H-InvDB links GTOP GTOP

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
303 .. 303 G/A rs200716680 + 5'UTR
344 .. 344 G/A rs139319429 + CDS Nonsynonymous[Val9Ile]
396 .. 396 C/G rs77660903 + CDS Nonsynonymous[Thr26Arg]
406 .. 406 T/G rs140996570 + CDS Synonymous[Val29Val]
417 .. 417 T/C rs115636787 + CDS Nonsynonymous[Ile33Thr]
606 .. 606 T/G rs143470699 + CDS Nonsynonymous[Ile96Arg]
608 .. 608 T/C rs201680913 + CDS Nonsynonymous[Ser97Pro]
664 .. 664 A/C rs150951840 + CDS Nonsynonymous[Glu115Asp]
695 .. 695 G/A rs143615820 + CDS Nonsynonymous[Glu126Lys]
747 .. 747 A/C rs201209663 + CDS Nonsynonymous[Gln143Pro]
885 .. 885 G/A rs144742726 + CDS Nonsynonymous[Arg189His]
1127 .. 1127 A/G rs961360 - CDS Nonsynonymous[Met270Val]
1238 .. 1238 G/A rs202129033 + CDS Nonsynonymous[Glu307Lys]
1247 .. 1247 A/C rs34088964 - CDS Nonsynonymous[Ile310Leu]
1268 .. 1268 G/A rs139991249 + CDS Nonsynonymous[Asp317Asn]
1299 .. 1299 G/A rs202036518 + CDS Nonsynonymous[Arg327His]
1362 .. 1362 C/G rs114219457 + CDS Nonsynonymous[Thr348Ser]
1449 .. 1449 C/T rs182409818 + CDS Nonsynonymous[Thr377Ile]
1586 .. 1586 C/T rs199860629 + CDS Nonsynonymous[His423Tyr]
1709 .. 1709 G/A rs140932904 + CDS Nonsynonymous[Ala464Thr]
1749 .. 1749 C/G rs147536237 + CDS Nonsynonymous[Ala477Gly]
1750 .. 1750 G/A rs149874194 + CDS Synonymous[Ala477Ala]
1753 .. 1753 A/C rs144901752 + CDS Synonymous[Ala478Ala]
1754 .. 1754 G/C rs143277081 + CDS Nonsynonymous[Gly479Arg]
1788 .. 1788 A/G rs116803765 + CDS Nonsynonymous[Gln490Arg]
1791 .. 1791 C/T rs140890871 + CDS Nonsynonymous[Thr491Ile]
1848 .. 1848 C/T rs150394823 + CDS Nonsynonymous[Thr510Ile]
1906 .. 1906 A/T rs13425947 + CDS Synonymous[Pro529Pro]
1960 .. 1960 T/C rs139193845 + CDS Synonymous[Ser547Ser]
2020 .. 2020 C/T rs147519491 + CDS Synonymous[Ala567Ala]
2064 .. 2064 C/G rs201789029 + CDS Nonsynonymous[Ser582Cys]
2087 .. 2087 C/A rs112729561 + CDS Nonsynonymous[Pro590Thr]
2089 .. 2089 T/C rs201061461 + CDS Synonymous[Pro590Pro]
2097 .. 2097 A/G rs150498555 + CDS Nonsynonymous[His593Arg]
2101 .. 2101 T/C rs200431099 + CDS Synonymous[Pro594Pro]
2124 .. 2124 C/T rs139457585 + CDS Nonsynonymous[Pro602Leu]
2134 .. 2134 T/C rs111235534 + CDS Synonymous[Pro605Pro]
2185 .. 2185 T/A rs202173447 + CDS Synonymous[Gly622Gly]
2217 .. 2217 A/C rs2305165 - CDS Nonsynonymous[Gln633Pro]
2264 .. 2264 G/A rs144077610 + CDS Nonsynonymous[Ala649Thr]
2274 .. 2274 A/G rs139502420 + CDS Nonsynonymous[His652Arg]
2300 .. 2300 C/T rs114677169 + CDS Nonsynonymous[Arg661Cys]
2304 .. 2304 C/T rs151233134 + CDS Nonsynonymous[Pro662Leu]
2358 .. 2358 C/T rs199515262 + CDS Nonsynonymous[Ala680Val]
2359 .. 2359 G/A rs139125340 + CDS Synonymous[Ala680Ala]
2415 .. 2415 T/G rs201906607 + CDS Nonsynonymous[Val699Gly]
2440 .. 2440 G/C rs143127486 + CDS Nonsynonymous[Gln707His]
2446 .. 2446 A/G rs149624809 + CDS Synonymous[Leu709Leu]
2539 .. 2539 A/G rs144388261 + CDS Synonymous[Gln740Gln]
2615 .. 2615 C/A rs76298784 + CDS Nonsynonymous[Pro766Thr]
2680 .. 2680 T/C rs199864603 + CDS Synonymous[Ser787Ser]
2733 .. 2733 C/T rs200294484 + CDS Nonsynonymous[Thr805Ile]
2766 .. 2766 G/A rs199587789 + CDS Nonsynonymous[Gly816Asp]
2780 .. 2780 G/A rs144042865 + CDS Nonsynonymous[Ala821Thr]
2789 .. 2789 C/A rs139565775 + CDS Nonsynonymous[Pro824Thr]
2868 .. 2868 C/T rs145608320 + CDS Nonsynonymous[Pro850Leu]
2869 .. 2869 G/A rs147882808 + CDS Synonymous[Pro850Pro]
2900 .. 2900 C/T rs143703596 + CDS Nonsynonymous[His861Tyr]
2905 .. 2905 G/A rs200624357 + CDS Synonymous[Gln862Gln]
2943 .. 2943 A/G rs148125749 + CDS Nonsynonymous[Asn875Ser]
2974 .. 2974 C/G rs115242070 + CDS Nonsynonymous[Ser885Arg]
2987 .. 2987 C/T rs201494950 + CDS Nonsynonymous[Pro890Ser]
3092 .. 3092 G/A rs116821936 + CDS Nonsynonymous[Gly925Arg]
3142 .. 3142 T/C rs199595729 + CDS Synonymous[Asn941Asn]
3160 .. 3160 C/T rs35003255 - CDS Synonymous[His947His]
3255 .. 3255 C/T rs115519111 + CDS Nonsynonymous[Ala979Val]
3276 .. 3276 A/T rs199512616 + CDS Nonsynonymous[Lys986Met]
3301 .. 3301 A/G rs113498203 + CDS Synonymous[Pro994Pro]
3402 .. 3402 G/A rs143951307 + CDS Nonsynonymous[Arg1028His]
3405 .. 3405 A/G rs148646134 + CDS Nonsynonymous[His1029Arg]
3424 .. 3424 T/G rs200059770 + CDS Nonsynonymous[Ser1035Arg]
3429 .. 3429 A/G rs72844194 + CDS Nonsynonymous[Asp1037Gly]
3443 .. 3443 C/A rs116105123 + CDS Nonsynonymous[Pro1042Thr]
3450 .. 3450 G/A rs114639828 + CDS Nonsynonymous[Arg1044His]
3541 .. 3541 T/G rs147866381 + CDS Nonsynonymous[Ile1074Met]
3545 .. 3545 T/G rs190617868 + CDS Nonsynonymous[Leu1076Val]
3579 .. 3579 A/G rs141539490 + CDS Nonsynonymous[Lys1087Arg]
3580 .. 3580 G/A rs145238803 + CDS Synonymous[Lys1087Lys]
3621 .. 3621 A/G rs116499913 + CDS Synonymous_atSTOP[*1101*]
3639 .. 3639 C/T rs182869080 + 3'UTR
3640 .. 3640 T/A rs78511053 + 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 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