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Q676U5 (A16L1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 85. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Autophagy-related protein 16-1
Alternative name(s):
APG16-like 1
Gene names
Name:ATG16L1
Synonyms:APG16L
ORF Names:UNQ9393/PRO34307
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length607 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Plays an essential role in autophagy By similarity.

Subunit structure

Homooligomer. Interacts with ATG5. Part of either the minor and major complexes respectively composed of 4 sets of ATG12-ATG5 and ATG16L1 (400 kDa) or 8 sets of ATG12-ATG5 and ATG16L1 (800 kDa) By similarity.

Subcellular location

Cytoplasm By similarity. Preautophagosomal structure membrane; Peripheral membrane protein By similarity. Note: Localized to preautophagosomal structure (PAS) where it is involved in the membrane targeting of ATG5 By similarity.

Involvement in disease

Genetic variations in ATG16L1 are associated with susceptibility to inflammatory bowel disease type 10 (IBD10) [MIM:611081]. IBD is characterized by a chronic relapsing intestinal inflammation. IBD is subdivided into Crohn disease (CD) and ulcerative colitis phenotypes. IBD10 individuals show the phenotype characteristic to CD. It may involve any part of the gastrointestinal tract, but most frequently the terminal ileum and colon. CD is commonly classified as autoimmune disease. Ref.2 Ref.10

Sequence similarities

Belongs to the WD repeat ATG16 family.

Contains 7 WD repeats.

Sequence caution

The sequence BAB15448.1 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.

The sequence BAB55412.1 differs from that shown. Reason: Erroneous initiation.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

MAP1LC3BQ9GZQ82EBI-535909,EBI-373144
MAP1LC3CQ9BXW44EBI-535909,EBI-2603996

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q676U5-1)

Also known as: APG16L beta;

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.
Isoform 2 (identifier: Q676U5-2)

The sequence of this isoform differs from the canonical sequence as follows:
     266-284: Missing.
Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Isoform 3 (identifier: Q676U5-3)

The sequence of this isoform differs from the canonical sequence as follows:
     443-470: IKTVFAGSSCNDIVCTEQCVMSGHFDKK → EEIQSLCLCICLDVSVEVCVCTSEPAFM
     471-607: Missing.
Note: No experimental confirmation available.
Isoform 4 (identifier: Q676U5-4)

The sequence of this isoform differs from the canonical sequence as follows:
     70-213: Missing.
     334-368: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 607607Autophagy-related protein 16-1
PRO_0000050848

Regions

Repeat320 – 35940WD 1
Repeat364 – 40340WD 2
Repeat406 – 44540WD 3
Repeat447 – 48438WD 4
Repeat486 – 52540WD 5
Repeat532 – 57342WD 6
Repeat575 – 60733WD 7
Coiled coil78 – 230153 Potential

Amino acid modifications

Modified residue2871Phosphoserine Ref.8 Ref.9
Modified residue2891Phosphoserine By similarity
Modified residue2901Phosphoserine Ref.8
Modified residue3041Phosphoserine Ref.8

Natural variations

Alternative sequence70 – 213144Missing in isoform 4.
VSP_013389
Alternative sequence266 – 28419Missing in isoform 2.
VSP_013386
Alternative sequence334 – 36835Missing in isoform 4.
VSP_013390
Alternative sequence443 – 47028IKTVF…HFDKK → EEIQSLCLCICLDVSVEVCV CTSEPAFM in isoform 3.
VSP_013387
Alternative sequence471 – 607137Missing in isoform 3.
VSP_013388
Natural variant3001T → A Associated with susceptibility to IBD10. Ref.1 Ref.2 Ref.10
Corresponds to variant rs2241880 [ dbSNP | Ensembl ].
VAR_021834
Natural variant3071E → K.
Corresponds to variant rs1866878 [ dbSNP | Ensembl ].
VAR_053386

Experimental info

Sequence conflict1511K → R in BAB55412. Ref.5
Sequence conflict3281V → A in BAB55412. Ref.5
Sequence conflict5291P → T in BAB55412. Ref.5

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (APG16L beta) [UniParc].

Last modified April 12, 2005. Version 2.
Checksum: 5A5816AE2CF03CA0

FASTA60768,265
        10         20         30         40         50         60 
MSSGLRAADF PRWKRHISEQ LRRRDRLQRQ AFEEIILQYN KLLEKSDLHS VLAQKLQAEK 

        70         80         90        100        110        120 
HDVPNRHEIS PGHDGTWNDN QLQEMAQLRI KHQEELTELH KKRGELAQLV IDLNNQMQRK 

       130        140        150        160        170        180 
DREMQMNEAK IAECLQTISD LETECLDLRT KLCDLERANQ TLKDEYDALQ ITFTALEGKL 

       190        200        210        220        230        240 
RKTTEENQEL VTRWMAEKAQ EANRLNAENE KDSRRRQARL QKELAEAAKE PLPVEQDDDI 

       250        260        270        280        290        300 
EVIVDETSDH TEETSPVRAI SRAATKRLSQ PAGGLLDSIT NIFGRRSVSS FPVPQDNVDT 

       310        320        330        340        350        360 
HPGSGKEVRV PATALCVFDA HDGEVNAVQF SPGSRLLATG GMDRRVKLWE VFGEKCEFKG 

       370        380        390        400        410        420 
SLSGSNAGIT SIEFDSAGSY LLAASNDFAS RIWTVDDYRL RHTLTGHSGK VLSAKFLLDN 

       430        440        450        460        470        480 
ARIVSGSHDR TLKLWDLRSK VCIKTVFAGS SCNDIVCTEQ CVMSGHFDKK IRFWDIRSES 

       490        500        510        520        530        540 
IVREMELLGK ITALDLNPER TELLSCSRDD LLKVIDLRTN AIKQTFSAPG FKCGSDWTRV 

       550        560        570        580        590        600 
VFSPDGSYVA AGSAEGSLYI WSVLTGKVEK VLSKQHSSSI NAVAWSPSGS HVVSVDKGCK 


AVLWAQY

« Hide

Isoform 2 [UniParc].

Checksum: 168A0E53B2190149
Show »

FASTA58866,296
Isoform 3 [UniParc].

Checksum: 7598952D2C1F2A79
Show »

FASTA47053,220
Isoform 4 [UniParc].

Checksum: E4F476255CDCA0A7
Show »

FASTA42847,686

References

« Hide 'large scale' references
[1]"Cloning and analysis of human Apg16L."
Zheng H., Ji C., Li J., Jiang H., Ren M., Lu Q., Gu S., Mao Y., Xie Y.
DNA Seq. 15:303-305(2004) [PubMed: 15620219] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT ALA-300.
Tissue: Fetal brain.
[2]"A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1."
Hampe J., Franke A., Rosenstiel P., Till A., Teuber M., Huse K., Albrecht M., Mayr G., De La Vega F.M., Briggs J., Guenther S., Prescott N.J., Onnie C.M., Haesler R., Sipos B., Foelsch U.R., Lengauer T., Platzer M. expand/collapse author list , Mathew C.G., Krawczak M., Schreiber S.
Nat. Genet. 39:207-211(2007) [PubMed: 17200669] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), ASSOCIATION OF VARIANT ALA-300 WITH SUSCEPTIBILITY TO IBD10.
[3]"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment."
Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. expand/collapse author list , Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.
Genome Res. 13:2265-2270(2003) [PubMed: 12975309] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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. expand/collapse author list , 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: 14702039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 55-607 (ISOFORM 2).
Tissue: Brain, Placenta and Small intestine.
[6]"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: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 114-607 (ISOFORM 2).
Tissue: Mammary gland.
[7]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 513-607.
Tissue: Testis.
[8]"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra."
Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D.
J. Proteome Res. 6:4150-4162(2007) [PubMed: 17924679] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-287; SER-290 AND SER-304, MASS SPECTROMETRY.
Tissue: Cervix carcinoma.
[9]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-287, MASS SPECTROMETRY.
Tissue: Cervix carcinoma.
[10]"Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis."
Rioux J.D., Xavier R.J., Taylor K.D., Silverberg M.S., Goyette P., Huett A., Green T., Kuballa P., Barmada M.M., Datta L.W., Shugart Y.Y., Griffiths A.M., Targan S.R., Ippoliti A.F., Bernard E.-J., Mei L., Nicolae D.L., Regueiro M. expand/collapse author list , Schumm L.P., Steinhart A.H., Rotter J.I., Duerr R.H., Cho J.H., Daly M.J., Brant S.R.
Nat. Genet. 39:596-604(2007) [PubMed: 17435756] [Abstract]
Cited for: ASSOCIATION OF VARIANT ALA-300 WITH SUSCEPTIBILITY TO IBD10.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AY398617 mRNA. Translation: AAR32130.1.
EF079889 mRNA. Translation: ABN48554.1.
AY358182 mRNA. Translation: AAQ88549.1.
AK026330 mRNA. Translation: BAB15448.1. Sequence problems.
AK027854 mRNA. Translation: BAB55412.1. Different initiation.
AK123876 mRNA. Translation: BAC85713.1.
CH471063 Genomic DNA. Translation: EAW71034.1.
BC071846 mRNA. Translation: AAH71846.1.
AL834526 mRNA. Translation: CAD39182.1.
IPIIPI00432751.
IPI00446614.
IPI00470446.
IPI00555905.
RefSeqNP_001177195.1. NM_001190266.1.
NP_001177196.1. NM_001190267.1.
NP_060444.3. NM_017974.3.
NP_110430.5. NM_030803.6.
NP_942593.2. NM_198890.2.
UniGeneHs.529322.

3D structure databases

ProteinModelPortalQ676U5.
SMRQ676U5. Positions 310-606.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-27552N.
IntActQ676U5. 22 interactions.
MINTMINT-1141152.
STRINGQ676U5.

PTM databases

PhosphoSiteQ676U5.

Polymorphism databases

DMDM62510482.

Proteomic databases

PRIDEQ676U5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000392017; ENSP00000375872; ENSG00000085978.
GeneID55054.
KEGGhsa:55054.
UCSCuc002vty.1. human.
uc002vtz.1. human.
uc002vua.1. human.

Organism-specific databases

CTD55054.
GeneCardsGC02P234118.
HGNCHGNC:21498. ATG16L1.
HPAHPA012577.
MIM610767. gene.
611081. phenotype.
neXtProtNX_Q676U5.
Orphanet206. Crohn disease.
GenAtlasSearch...

Phylogenomic databases

eggNOGprNOG09453.
HOVERGENHBG050534.
OrthoDBEOG4SXNC8.
PhylomeDBQ676U5.

Gene expression databases

ArrayExpressQ676U5.
BgeeQ676U5.
CleanExHS_ATG16L1.
GenevestigatorQ676U5.
GermOnlineENSG00000085978. Homo sapiens.

Family and domain databases

InterProIPR013923. Autophagy-rel_prot_16.
IPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR011046. WD40_repeat-like_dom.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
Gene3DG3DSA:2.130.10.10. WD40/YVTN_repeat-like. 2 hits.
PfamPF08614. ATG16. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]
PRINTSPR00320. GPROTEINBRPT.
SMARTSM00320. WD40. 7 hits.
[Graphical view]
SUPFAMSSF50978. WD40_like. 1 hit.
PROSITEPS00678. WD_REPEATS_1. 3 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio58531.
SOURCESearch...

Entry information

Entry nameA16L1_HUMAN
AccessionPrimary (citable) accession number: Q676U5
Secondary accession number(s): A3EXK9 expand/collapse secondary AC list , Q6IPN1, Q6UXW4, Q6ZVZ5, Q8NCY2, Q96JV5, Q9H619
Entry history
Integrated into UniProtKB/Swiss-Prot: April 12, 2005
Last sequence update: April 12, 2005
Last modified: January 25, 2012
This is version 85 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents