TT39B_HUMAN
ID TT39B_HUMAN Reviewed; 682 AA.
AC Q5VTQ0; A5PLN1; B4DQ10; B4DQX4; B4DW93; Q8IVR7; Q8IXZ6; Q8N267;
DT 26-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 18-APR-2012, sequence version 4.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Tetratricopeptide repeat protein 39B;
DE Short=TPR repeat protein 39B;
GN Name=TTC39B {ECO:0000312|HGNC:HGNC:23704}; Synonyms=C9orf52;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 3 AND 5), NUCLEOTIDE
RP SEQUENCE [LARGE SCALE MRNA] OF 27-682 (ISOFORM 1), NUCLEOTIDE SEQUENCE
RP [LARGE SCALE MRNA] OF 37-682 (ISOFORM 6), AND VARIANT VAL-420.
RC TISSUE=Blood, Synovium, Teratocarcinoma, and Tongue;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15164053; DOI=10.1038/nature02465;
RA Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L.,
RA Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R.,
RA Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S.,
RA Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K.,
RA Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y.,
RA Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C.,
RA Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E.,
RA Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M.,
RA Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J.,
RA Frankish A., Frankland J.A., French L., Fricker D.G., Garner P.,
RA Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S.,
RA Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E.,
RA Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D.,
RA Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E.,
RA Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K.,
RA Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S.,
RA Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J.,
RA Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E.,
RA McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V.,
RA Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S.,
RA Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K.,
RA Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J.,
RA Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M.,
RA West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L.,
RA Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M.,
RA Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J.,
RA Dunham I.;
RT "DNA sequence and analysis of human chromosome 9.";
RL Nature 429:369-374(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2; 4 AND 7), AND VARIANT
RP VAL-420.
RC TISSUE=Blood, and Brain;
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).
CC -!- FUNCTION: Regulates high density lipoprotein (HDL) cholesterol
CC metabolism by promoting the ubiquitination and degradation of the
CC oxysterols receptors LXR (NR1H2 and NR1H3).
CC {ECO:0000250|UniProtKB:Q8BYY4}.
CC -!- INTERACTION:
CC Q5VTQ0; O95292: VAPB; NbExp=3; IntAct=EBI-4289975, EBI-1188298;
CC Q5VTQ0-4; P50222: MEOX2; NbExp=3; IntAct=EBI-10247626, EBI-748397;
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=7;
CC Name=1;
CC IsoId=Q5VTQ0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5VTQ0-2; Sequence=VSP_026355;
CC Name=3;
CC IsoId=Q5VTQ0-3; Sequence=VSP_042802;
CC Name=4;
CC IsoId=Q5VTQ0-4; Sequence=VSP_042801;
CC Name=5;
CC IsoId=Q5VTQ0-5; Sequence=VSP_042799;
CC Name=6;
CC IsoId=Q5VTQ0-6; Sequence=VSP_042800;
CC Name=7;
CC IsoId=Q5VTQ0-7; Sequence=VSP_042798, VSP_042803;
CC -!- SIMILARITY: Belongs to the TTC39 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH42417.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAI42986.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAC03603.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAG60772.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK091187; BAC03603.1; ALT_INIT; mRNA.
DR EMBL; AK298581; BAG60772.1; ALT_INIT; mRNA.
DR EMBL; AK298998; BAG61086.1; -; mRNA.
DR EMBL; AK301427; BAG62955.1; -; mRNA.
DR EMBL; AL591393; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC038592; AAH38592.1; -; mRNA.
DR EMBL; BC042417; AAH42417.1; ALT_INIT; mRNA.
DR EMBL; BC142985; AAI42986.1; ALT_INIT; mRNA.
DR CCDS; CCDS55294.1; -. [Q5VTQ0-5]
DR RefSeq; NP_001161811.1; NM_001168339.1. [Q5VTQ0-4]
DR RefSeq; NP_001161812.1; NM_001168340.1. [Q5VTQ0-3]
DR RefSeq; NP_001161813.1; NM_001168341.1. [Q5VTQ0-6]
DR RefSeq; NP_001161814.1; NM_001168342.1. [Q5VTQ0-5]
DR RefSeq; NP_689787.2; NM_152574.2. [Q5VTQ0-1]
DR RefSeq; XP_011516034.1; XM_011517732.2. [Q5VTQ0-2]
DR RefSeq; XP_016869800.1; XM_017014311.1. [Q5VTQ0-2]
DR RefSeq; XP_016869801.1; XM_017014312.1. [Q5VTQ0-2]
DR AlphaFoldDB; Q5VTQ0; -.
DR SMR; Q5VTQ0; -.
DR BioGRID; 127655; 16.
DR DIP; DIP-62094N; -.
DR IntAct; Q5VTQ0; 5.
DR STRING; 9606.ENSP00000422496; -.
DR iPTMnet; Q5VTQ0; -.
DR PhosphoSitePlus; Q5VTQ0; -.
DR BioMuta; TTC39B; -.
DR DMDM; 384872705; -.
DR EPD; Q5VTQ0; -.
DR jPOST; Q5VTQ0; -.
DR MassIVE; Q5VTQ0; -.
DR MaxQB; Q5VTQ0; -.
DR PaxDb; Q5VTQ0; -.
DR PeptideAtlas; Q5VTQ0; -.
DR PRIDE; Q5VTQ0; -.
DR ProteomicsDB; 65339; -. [Q5VTQ0-1]
DR ProteomicsDB; 65340; -. [Q5VTQ0-2]
DR ProteomicsDB; 65341; -. [Q5VTQ0-3]
DR ProteomicsDB; 65342; -. [Q5VTQ0-4]
DR ProteomicsDB; 65343; -. [Q5VTQ0-5]
DR ProteomicsDB; 65344; -. [Q5VTQ0-6]
DR ProteomicsDB; 65345; -. [Q5VTQ0-7]
DR Antibodypedia; 24508; 102 antibodies from 22 providers.
DR DNASU; 158219; -.
DR Ensembl; ENST00000297615.9; ENSP00000297615.5; ENSG00000155158.20. [Q5VTQ0-6]
DR Ensembl; ENST00000380850.8; ENSP00000370231.4; ENSG00000155158.20. [Q5VTQ0-3]
DR Ensembl; ENST00000507285.5; ENSP00000426539.1; ENSG00000155158.20. [Q5VTQ0-5]
DR Ensembl; ENST00000507993.5; ENSP00000423392.1; ENSG00000155158.20. [Q5VTQ0-5]
DR Ensembl; ENST00000512701.6; ENSP00000422496.1; ENSG00000155158.20. [Q5VTQ0-1]
DR GeneID; 158219; -.
DR KEGG; hsa:158219; -.
DR MANE-Select; ENST00000512701.7; ENSP00000422496.2; NM_152574.3; NP_689787.3.
DR UCSC; uc003zlr.3; human. [Q5VTQ0-1]
DR CTD; 158219; -.
DR DisGeNET; 158219; -.
DR GeneCards; TTC39B; -.
DR HGNC; HGNC:23704; TTC39B.
DR HPA; ENSG00000155158; Low tissue specificity.
DR MIM; 613574; gene.
DR neXtProt; NX_Q5VTQ0; -.
DR OpenTargets; ENSG00000155158; -.
DR PharmGKB; PA162407261; -.
DR VEuPathDB; HostDB:ENSG00000155158; -.
DR eggNOG; KOG3783; Eukaryota.
DR GeneTree; ENSGT00950000182917; -.
DR HOGENOM; CLU_010086_3_0_1; -.
DR InParanoid; Q5VTQ0; -.
DR OMA; ELMYVWN; -.
DR OrthoDB; 754120at2759; -.
DR PhylomeDB; Q5VTQ0; -.
DR TreeFam; TF313761; -.
DR PathwayCommons; Q5VTQ0; -.
DR SignaLink; Q5VTQ0; -.
DR BioGRID-ORCS; 158219; 7 hits in 1073 CRISPR screens.
DR ChiTaRS; TTC39B; human.
DR GenomeRNAi; 158219; -.
DR Pharos; Q5VTQ0; Tbio.
DR PRO; PR:Q5VTQ0; -.
DR Proteomes; UP000005640; Chromosome 9.
DR RNAct; Q5VTQ0; protein.
DR Bgee; ENSG00000155158; Expressed in epithelial cell of pancreas and 167 other tissues.
DR ExpressionAtlas; Q5VTQ0; baseline and differential.
DR Genevisible; Q5VTQ0; HS.
DR GO; GO:0042632; P:cholesterol homeostasis; ISS:UniProtKB.
DR GO; GO:0006629; P:lipid metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0010887; P:negative regulation of cholesterol storage; ISS:UniProtKB.
DR GO; GO:0010874; P:regulation of cholesterol efflux; ISS:UniProtKB.
DR GO; GO:0090181; P:regulation of cholesterol metabolic process; ISS:UniProtKB.
DR Gene3D; 1.25.40.10; -; 1.
DR InterPro; IPR019412; Iml2/TPR_39.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR InterPro; IPR019734; TPR_repeat.
DR InterPro; IPR034305; TTC39B.
DR PANTHER; PTHR31859; PTHR31859; 1.
DR PANTHER; PTHR31859:SF4; PTHR31859:SF4; 1.
DR Pfam; PF10300; DUF3808; 1.
DR Pfam; PF13174; TPR_6; 1.
DR SMART; SM00028; TPR; 3.
PE 1: Evidence at protein level;
KW Alternative splicing; Lipid metabolism; Reference proteome; Repeat;
KW TPR repeat; Ubl conjugation pathway.
FT CHAIN 1..682
FT /note="Tetratricopeptide repeat protein 39B"
FT /id="PRO_0000292000"
FT REPEAT 393..426
FT /note="TPR 1"
FT REPEAT 626..659
FT /note="TPR 2"
FT VAR_SEQ 1..483
FT /note="Missing (in isoform 7)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_042798"
FT VAR_SEQ 1..165
FT /note="Missing (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_042799"
FT VAR_SEQ 1..97
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_026355"
FT VAR_SEQ 92..161
FT /note="ISSHSDMATSSLHFASCDTQQAPRQRGASTVSSSSSTKVDLKSGLEECAVAL
FT NLFLSNKFTDALELLRPW -> M (in isoform 6)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_042800"
FT VAR_SEQ 206..207
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_042801"
FT VAR_SEQ 392..411
FT /note="GSLVLFYHARIELLKGNLEE -> VRSVFQS (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_042802"
FT VAR_SEQ 484..495
FT /note="VVATNENVVTLF -> MTFLWGWAGVLH (in isoform 7)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_042803"
FT VARIANT 128
FT /note="T -> P (in dbSNP:rs10961917)"
FT /id="VAR_054078"
FT VARIANT 420
FT /note="I -> V (in dbSNP:rs1407977)"
FT /evidence="ECO:0000269|PubMed:14702039,
FT ECO:0000269|PubMed:15489334"
FT /id="VAR_032926"
FT CONFLICT 7
FT /note="C -> Y (in Ref. 1; BAG61086)"
FT /evidence="ECO:0000305"
FT CONFLICT 329
FT /note="S -> F (in Ref. 1; BAG61086)"
FT /evidence="ECO:0000305"
FT CONFLICT 496
FT /note="R -> S (in Ref. 1; BAG60772)"
FT /evidence="ECO:0000305"
FT CONFLICT 500
FT /note="S -> G (in Ref. 1; BAG60772)"
FT /evidence="ECO:0000305"
FT CONFLICT 667
FT /note="F -> L (in Ref. 3; AAI42986)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 682 AA; 76956 MW; 6A61462D635A4373 CRC64;
MDAVLACRLR GRGNRVAALR PRPRPGGSAG PSPFALLCAG LSPEPRAGVG SEFPAWFLGG
SSQRRNMALL GSRAELEADE DVFEDALETI SISSHSDMAT SSLHFASCDT QQAPRQRGAS
TVSSSSSTKV DLKSGLEECA VALNLFLSNK FTDALELLRP WAKESMYHAL GYSTIVVLQA
VLTFEQQDIQ NGISAMKDAL QTCQKYRKKY TVVESFSSLL SRGSLEQLSE EEMHAEICYA
ECLLQKAALT FVQDENMINF IKGGLKIRTS YQIYKECLSI LHEIQKNKLQ QEFFYEFEGG
VKLGSGAFNL MLSLLPARII RLLEFIGFSG NRELGLLQLR EGASGRSMRS ALCCLTILAF
HTYISLILGT GEVNVAEAER LLAPFLQQFP NGSLVLFYHA RIELLKGNLE EAQEVFQKCI
SVQEEWKQFH HLCYWELMWI NVFQQNWMQA YYYSDLLCKE SKWSKATYVF LKAAILSMLP
EEDVVATNEN VVTLFRQVDS LKQRIAGKSI PTEKFAVRKA RRYSASLPAP VKLILPALEM
MYVWNGFSIV SKRKDLSENL LVTVEKAEAA LQSQNFNSFS VDDECLVKLL KGCCLKNLQR
PLQAELCYNH VVESEKLLKY DHYLVPFTLF ELASLYKSQG EIDKAIKFLE TARNNYKDYS
LESRLHFRIQ AALHLWRKPS SD
