YIF1B_MOUSE
ID YIF1B_MOUSE Reviewed; 311 AA.
AC Q9CX30; Q32M25; Q3UXJ5;
DT 23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT 23-OCT-2007, sequence version 2.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Protein YIF1B {ECO:0000305};
DE AltName: Full=YIP1-interacting factor homolog B;
GN Name=Yif1b {ECO:0000312|MGI:MGI:1924504};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=C57BL/6J; TISSUE=Embryo, and Muellerian duct;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, PHOSPHORYLATION [LARGE SCALE
RP ANALYSIS] AT THR-12, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
RP ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [5]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=26077767; DOI=10.1111/tra.12306;
RA Alterio J., Masson J., Diaz J., Chachlaki K., Salman H., Areias J.,
RA Al Awabdh S., Emerit M.B., Darmon M.;
RT "Yif1B Is Involved in the Anterograde Traffic Pathway and the Golgi
RT Architecture.";
RL Traffic 16:978-993(2015).
RN [6]
RP FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=33103737; DOI=10.1093/brain/awaa235;
RA Diaz J., Gerard X., Emerit M.B., Areias J., Geny D., Degardin J.,
RA Simonutti M., Guerquin M.J., Collin T., Viollet C., Billard J.M., Metin C.,
RA Hubert L., Larti F., Kahrizi K., Jobling R., Agolini E., Shaheen R.,
RA Zigler A., Rouiller-Fabre V., Rozet J.M., Picaud S., Novelli A.,
RA Alameer S., Najmabadi H., Cohn R., Munnich A., Barth M., Lugli L.,
RA Alkuraya F.S., Blaser S., Gashlan M., Besmond C., Darmon M., Masson J.;
RT "YIF1B mutations cause a post-natal neurodevelopmental syndrome associated
RT with Golgi and primary cilium alterations.";
RL Brain 143:2911-2928(2020).
CC -!- FUNCTION: Functions in endoplasmic reticulum to Golgi vesicle-mediated
CC transport and regulates the proper organization of the endoplasmic
CC reticulum and the Golgi (PubMed:26077767, PubMed:33103737). Plays a key
CC role in targeting to neuronal dendrites receptors such as HTR1A (By
CC similarity). Also plays a role in primary cilium and sperm flagellum
CC assembly probably through protein transport to these compartments
CC (PubMed:33103737). {ECO:0000250|UniProtKB:Q6PEC3,
CC ECO:0000269|PubMed:26077767, ECO:0000269|PubMed:33103737}.
CC -!- SUBUNIT: Interacts with HTR1A (via C-terminus) (By similarity).
CC Interacts with ABCB9 (via TMD0); this interaction allows (but is not
CC essential) the ER-to-Golgi trafficking and strongly depends on a salt
CC bridge within TMD0 (By similarity). {ECO:0000250|UniProtKB:Q5BJH7,
CC ECO:0000250|UniProtKB:Q6PEC3}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:33103737}; Multi-pass membrane protein
CC {ECO:0000255}. Golgi apparatus membrane {ECO:0000269|PubMed:33103737};
CC Multi-pass membrane protein {ECO:0000255}. Note=Shuttles between the
CC endoplasmic reticulum, the intermediate compartment and the Golgi
CC apparatus. {ECO:0000250|UniProtKB:Q6PEC3}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9CX30-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9CX30-2; Sequence=VSP_028656;
CC -!- TISSUE SPECIFICITY: Highly expressed in brain. Expressed in Purkinje
CC cells of the cerebellum. {ECO:0000269|PubMed:33103737}.
CC -!- DISRUPTION PHENOTYPE: Homozygous knockout mice lacking Yif1b show
CC impaired visual perception associated with retinal dysfunction and
CC optic atrophy while no ventilator defects or increased susceptibility
CC to seizures is observed. Some deficits in fine motor skills and
CC coordination are also observed. Mutant mice have delayed cerebral
CC myelination, enlarged ventricles, and cerebellar atrophy associated
CC with a reduction in the number of Purkinje cells due to
CC neurodegeneration and necrosis. Purkinje cells show fragmentation of
CC the Golgi apparatus, large autophagosome-like vacuoles, and alteration
CC of the endoplasmic reticulum with dilated cisternae. Male knockout mice
CC are infertile due to abnormal spermatozoa flagella that show
CC microtubule disorganization. Primary cilium abnormalities are also
CC observed in cerebellar Purkinje cells and hippocampal pyramidal cells,
CC for instance. {ECO:0000269|PubMed:33103737}.
CC -!- SIMILARITY: Belongs to the YIF1 family. {ECO:0000305}.
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DR EMBL; AK020444; BAB32103.1; -; mRNA.
DR EMBL; AK135529; BAE22568.1; -; mRNA.
DR EMBL; BC109331; AAI09332.1; -; mRNA.
DR CCDS; CCDS21069.1; -. [Q9CX30-1]
DR CCDS; CCDS52171.1; -. [Q9CX30-2]
DR RefSeq; NP_001103671.1; NM_001110201.1. [Q9CX30-2]
DR RefSeq; NP_084163.2; NM_029887.3. [Q9CX30-1]
DR AlphaFoldDB; Q9CX30; -.
DR BioGRID; 218579; 6.
DR IntAct; Q9CX30; 2.
DR STRING; 10090.ENSMUSP00000032809; -.
DR iPTMnet; Q9CX30; -.
DR PhosphoSitePlus; Q9CX30; -.
DR EPD; Q9CX30; -.
DR MaxQB; Q9CX30; -.
DR PaxDb; Q9CX30; -.
DR PeptideAtlas; Q9CX30; -.
DR PRIDE; Q9CX30; -.
DR ProteomicsDB; 299611; -. [Q9CX30-1]
DR ProteomicsDB; 299612; -. [Q9CX30-2]
DR Antibodypedia; 30011; 125 antibodies from 19 providers.
DR DNASU; 77254; -.
DR Ensembl; ENSMUST00000032809; ENSMUSP00000032809; ENSMUSG00000030588. [Q9CX30-1]
DR Ensembl; ENSMUST00000108238; ENSMUSP00000103873; ENSMUSG00000030588. [Q9CX30-2]
DR GeneID; 77254; -.
DR KEGG; mmu:77254; -.
DR UCSC; uc009gbh.2; mouse. [Q9CX30-2]
DR UCSC; uc009gbi.2; mouse. [Q9CX30-1]
DR CTD; 90522; -.
DR MGI; MGI:1924504; Yif1b.
DR VEuPathDB; HostDB:ENSMUSG00000030588; -.
DR eggNOG; KOG3094; Eukaryota.
DR GeneTree; ENSGT00390000009423; -.
DR HOGENOM; CLU_047877_1_1_1; -.
DR InParanoid; Q9CX30; -.
DR OMA; FMWLLTR; -.
DR OrthoDB; 1256839at2759; -.
DR PhylomeDB; Q9CX30; -.
DR TreeFam; TF314528; -.
DR BioGRID-ORCS; 77254; 1 hit in 71 CRISPR screens.
DR ChiTaRS; Yif1b; mouse.
DR PRO; PR:Q9CX30; -.
DR Proteomes; UP000000589; Chromosome 7.
DR RNAct; Q9CX30; protein.
DR Bgee; ENSMUSG00000030588; Expressed in humerus cartilage element and 225 other tissues.
DR ExpressionAtlas; Q9CX30; baseline and differential.
DR Genevisible; Q9CX30; MM.
DR GO; GO:0030134; C:COPII-coated ER to Golgi transport vesicle; IBA:GO_Central.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:UniProtKB.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IBA:GO_Central.
DR GO; GO:0005793; C:endoplasmic reticulum-Golgi intermediate compartment; IDA:UniProtKB.
DR GO; GO:0005794; C:Golgi apparatus; IDA:UniProtKB.
DR GO; GO:0030173; C:integral component of Golgi membrane; IBA:GO_Central.
DR GO; GO:0060271; P:cilium assembly; IMP:UniProtKB.
DR GO; GO:0006888; P:endoplasmic reticulum to Golgi vesicle-mediated transport; IMP:UniProtKB.
DR GO; GO:0006612; P:protein targeting to membrane; IMP:UniProtKB.
DR GO; GO:0120316; P:sperm flagellum assembly; IMP:UniProtKB.
DR InterPro; IPR005578; Yif1_fam.
DR PANTHER; PTHR14083; PTHR14083; 1.
DR Pfam; PF03878; YIF1; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Endoplasmic reticulum; Golgi apparatus;
KW Membrane; Phosphoprotein; Protein transport; Reference proteome;
KW Transmembrane; Transmembrane helix; Transport.
FT CHAIN 1..311
FT /note="Protein YIF1B"
FT /id="PRO_0000307259"
FT TOPO_DOM 1..153
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 154..174
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 175..189
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 190..210
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 211..216
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 217..237
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 238
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 239..259
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 260..289
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 290..310
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 311
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT REGION 1..57
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:17242355"
FT MOD_RES 12
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17242355"
FT MOD_RES 64
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q5BJH7"
FT VAR_SEQ 16..18
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334,
FT ECO:0000303|PubMed:16141072"
FT /id="VSP_028656"
FT CONFLICT 160
FT /note="A -> G (in Ref. 1; BAB32103)"
FT /evidence="ECO:0000305"
FT CONFLICT 197
FT /note="E -> K (in Ref. 1; BAB32103)"
FT /evidence="ECO:0000305"
FT CONFLICT 277
FT /note="V -> E (in Ref. 1; BAE22568)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 311 AA; 33983 MW; BFC353B2D2C37074 CRC64;
MHATGLAAPA GTPRLRKWPS KRRVPVSQPG MADPHQFFDD TSSAPSRGYG GQPSPGGLGY
PPSSSDAAFL AAPMSNMAMV YGSSLAAQGK ELVDKNIDRF IPVSKLKYYF AVDTVYVGKK
LGLLVFPYLH QDWEVQYQQD TPVAPRFDIN APDLYIPAMA FITYILVAGL ALGTQDRFSP
DLLGLQASSA LAWLTLEVVA ILLSLYLVTV NTDLTTIDLV AFLGYKYVGM IGGVLTGLLF
GKIGYYLVLA WCCVSIFVFM IRTLRLKILA QAAAEGVPVR GARNQLRMYL TMAVAAAQPV
LMYWLTFHLV R
