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Protein

piRNA biogenesis protein EXD1

Gene

EXD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposable elements, preventing their mobilization, which is essential for the germline integrity (By similarity). The PET complex is required during the secondary piRNAs metabolic process for the PIWIL2 slicing-triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA adapter. EXD1 is an inactive exonuclease (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Meiosis, RNA-mediated gene silencing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
piRNA biogenesis protein EXD1Curated
Alternative name(s):
Exonuclease 3'-5' domain-containing protein 1Imported
Exonuclease 3'-5' domain-like-containing protein 1Imported
Inactive exonuclease EXD1Curated
Gene namesi
Name:EXD1
Synonyms:EXDL1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

HGNCiHGNC:28507. EXD1.

Subcellular locationi

  • Cytoplasm By similarity

  • Note: Component of the meiotic nuage, also named P granule, a germ-cell-specific organelle required to repress transposon activity during meiosis.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164719420.

Polymorphism and mutation databases

BioMutaiEXD1.
DMDMi317373564.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 514514piRNA biogenesis protein EXD1PRO_0000337244Add
BLAST

Proteomic databases

EPDiQ8NHP7.
PaxDbiQ8NHP7.
PRIDEiQ8NHP7.

PTM databases

iPTMnetiQ8NHP7.
PhosphoSiteiQ8NHP7.

Expressioni

Gene expression databases

BgeeiQ8NHP7.
CleanExiHS_EXDL1.
ExpressionAtlasiQ8NHP7. baseline and differential.
GenevisibleiQ8NHP7. HS.

Organism-specific databases

HPAiHPA039388.

Interactioni

Subunit structurei

Homodimer (By similarity). Component of the PET complex, at least composed of EXD1, PIWIL2, TDRD12 and piRNAs (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
EML2O958343EBI-10192266,EBI-1054588

GO - Molecular functioni

Protein-protein interaction databases

BioGridi127804. 1 interaction.
IntActiQ8NHP7. 1 interaction.
STRINGi9606.ENSP00000321029.

Structurei

3D structure databases

ProteinModelPortaliQ8NHP7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini30 – 122933'-5' exonucleaseSequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi72 – 754Poly-Glu

Domaini

The 3'-5' exonuclease domain lacks the conserved Asp-Glu-Asp-Asp (DEDD) residues that coordinates divalent ions essential for exonuclease activity.By similarity

Sequence similaritiesi

Belongs to the EXD1 family.Curated
Contains 1 3'-5' exonuclease domain.Curated

Phylogenomic databases

eggNOGiKOG2405. Eukaryota.
ENOG4111GM1. LUCA.
GeneTreeiENSGT00390000003581.
HOGENOMiHOG000112411.
KOiK18740.
OMAiTCMELPE.
OrthoDBiEOG7WDN36.
PhylomeDBiQ8NHP7.
TreeFamiTF315023.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR002562. 3'-5'_exonuclease_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF01612. DNA_pol_A_exo1. 1 hit.
[Graphical view]
SMARTiSM00474. 35EXOc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8NHP7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEDSEFLAYV ELLDEVEQGS VRAKASSVSL HAERTWMEKM KVEDLNVCEP
60 70 80 90 100
ASPAPEAPAT SLLNDLKYSP SEEEEVTYTV INQFQQKFGA AILHIKKQNV
110 120 130 140 150
LSVAAEGANV CRHGKLCWLQ VATNCRVYLF DIFLLGSRAF HNGLQMILED
160 170 180 190 200
KRILKVIHDC RWLSDCLSHQ YGILLNNVFD TQVADVLQFS METGGYLPNC
210 220 230 240 250
ITTLQESLIK HLQVAPKYLS FLEKRQKLIQ ENPEVWFIRP VSPSLLKILA
260 270 280 290 300
LEATYLLPLR LALLDEMMSD LTTLVDGYLN TYREGSADRL GGTEPTCMEL
310 320 330 340 350
PEELLQLKDF QKQRREKAAR EYRVNAQGLL IRTVLQPKKL VTETAGKEEK
360 370 380 390 400
VKGFLFGKNF RIDKAPSFTS QDFHGDVNLL KEESLNKQAT NPQHLPPTEE
410 420 430 440 450
GETSEDSSNK LICTKSKGSE DQRITQKEHF MTPKHEFQAS LSLKEETEQL
460 470 480 490 500
LMVENKEDLK CTKQAVSMSS FPQETRVSPS DTFYPIRKTV VSTLPPCPAL
510
EKIDSWISPF LNLP
Length:514
Mass (Da):58,335
Last modified:January 11, 2011 - v4
Checksum:i77CDD6CF846886DA
GO
Isoform 2 (identifier: Q8NHP7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-229: MEDSEFLAYV...SFLEKRQKLI → MSHCAQPKTVIFFKVLLTVQRKLFYCL

Note: No experimental confirmation available.
Show »
Length:312
Mass (Da):35,585
Checksum:i0A0CC6FCB76AF7E2
GO
Isoform 3 (identifier: Q8NHP7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-9: MEDSEFLAY → MDPSSDYHFL...KLFFGHEIVN

Note: No experimental confirmation available.
Show »
Length:572
Mass (Da):64,822
Checksum:i5AFC09FE89114FFA
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti32 – 321A → T in BAF85213 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti489 – 4891T → A.1 Publication
Corresponds to variant rs522063 [ dbSNP | Ensembl ].
VAR_043676

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 229229MEDSE…RQKLI → MSHCAQPKTVIFFKVLLTVQ RKLFYCL in isoform 2. 1 PublicationVSP_033987Add
BLAST
Alternative sequencei1 – 99MEDSEFLAY → MDPSSDYHFLSQILWKRVKL TLVCGVFEGVLQHVDPNKIV VLKKVKNVETGRSVPGVKLF FGHEIVN in isoform 3. 1 PublicationVSP_054898

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK123414 mRNA. Translation: BAC85610.1.
AK292524 mRNA. Translation: BAF85213.1.
AK302864 mRNA. Translation: BAH13825.1.
AC012652 Genomic DNA. No translation available.
AC022408 Genomic DNA. No translation available.
BC030628 mRNA. Translation: AAH30628.2.
CCDSiCCDS10072.1. [Q8NHP7-1]
CCDS66738.1. [Q8NHP7-3]
RefSeqiNP_001273370.1. NM_001286441.1. [Q8NHP7-3]
NP_689809.2. NM_152596.3. [Q8NHP7-1]
XP_011519600.1. XM_011521298.1. [Q8NHP7-3]
UniGeneiHs.307999.

Genome annotation databases

EnsembliENST00000314992; ENSP00000321029; ENSG00000178997. [Q8NHP7-1]
ENST00000458580; ENSP00000415056; ENSG00000178997. [Q8NHP7-3]
GeneIDi161829.
KEGGihsa:161829.
UCSCiuc001znk.5. human. [Q8NHP7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK123414 mRNA. Translation: BAC85610.1.
AK292524 mRNA. Translation: BAF85213.1.
AK302864 mRNA. Translation: BAH13825.1.
AC012652 Genomic DNA. No translation available.
AC022408 Genomic DNA. No translation available.
BC030628 mRNA. Translation: AAH30628.2.
CCDSiCCDS10072.1. [Q8NHP7-1]
CCDS66738.1. [Q8NHP7-3]
RefSeqiNP_001273370.1. NM_001286441.1. [Q8NHP7-3]
NP_689809.2. NM_152596.3. [Q8NHP7-1]
XP_011519600.1. XM_011521298.1. [Q8NHP7-3]
UniGeneiHs.307999.

3D structure databases

ProteinModelPortaliQ8NHP7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi127804. 1 interaction.
IntActiQ8NHP7. 1 interaction.
STRINGi9606.ENSP00000321029.

PTM databases

iPTMnetiQ8NHP7.
PhosphoSiteiQ8NHP7.

Polymorphism and mutation databases

BioMutaiEXD1.
DMDMi317373564.

Proteomic databases

EPDiQ8NHP7.
PaxDbiQ8NHP7.
PRIDEiQ8NHP7.

Protocols and materials databases

DNASUi161829.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000314992; ENSP00000321029; ENSG00000178997. [Q8NHP7-1]
ENST00000458580; ENSP00000415056; ENSG00000178997. [Q8NHP7-3]
GeneIDi161829.
KEGGihsa:161829.
UCSCiuc001znk.5. human. [Q8NHP7-1]

Organism-specific databases

CTDi161829.
GeneCardsiEXD1.
HGNCiHGNC:28507. EXD1.
HPAiHPA039388.
neXtProtiNX_Q8NHP7.
PharmGKBiPA164719420.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2405. Eukaryota.
ENOG4111GM1. LUCA.
GeneTreeiENSGT00390000003581.
HOGENOMiHOG000112411.
KOiK18740.
OMAiTCMELPE.
OrthoDBiEOG7WDN36.
PhylomeDBiQ8NHP7.
TreeFamiTF315023.

Miscellaneous databases

ChiTaRSiEXD1. human.
GenomeRNAii161829.
NextBioi35480382.
PROiQ8NHP7.

Gene expression databases

BgeeiQ8NHP7.
CleanExiHS_EXDL1.
ExpressionAtlasiQ8NHP7. baseline and differential.
GenevisibleiQ8NHP7. HS.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR002562. 3'-5'_exonuclease_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF01612. DNA_pol_A_exo1. 1 hit.
[Graphical view]
SMARTiSM00474. 35EXOc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3), VARIANT ALA-489.
    Tissue: Hippocampus and Testis.
  2. "Analysis of the DNA sequence and duplication history of human chromosome 15."
    Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A.
    , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
    Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Testis.

Entry informationi

Entry nameiEXD1_HUMAN
AccessioniPrimary (citable) accession number: Q8NHP7
Secondary accession number(s): A8K909, B7Z839, Q6ZW94
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: January 11, 2011
Last modified: May 11, 2016
This is version 111 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.