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Protein

CAP-Gly domain-containing linker protein 4

Gene

CLIP4

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

Names & Taxonomyi

Protein namesi
Recommended name:
CAP-Gly domain-containing linker protein 4
Alternative name(s):
Restin-like protein 2
Gene namesi
Name:CLIP4
Synonyms:RSNL2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:26108. CLIP4.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162382440.

Polymorphism and mutation databases

BioMutaiCLIP4.
DMDMi60390950.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 705705CAP-Gly domain-containing linker protein 4PRO_0000083529Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei557 – 5571PhosphoserineBy similarity
Modified residuei609 – 6091PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8N3C7.
MaxQBiQ8N3C7.
PaxDbiQ8N3C7.
PeptideAtlasiQ8N3C7.
PRIDEiQ8N3C7.
TopDownProteomicsiQ8N3C7-4. [Q8N3C7-4]

PTM databases

iPTMnetiQ8N3C7.
PhosphoSiteiQ8N3C7.

Expressioni

Gene expression databases

BgeeiQ8N3C7.
CleanExiHS_CLIP4.
ExpressionAtlasiQ8N3C7. baseline and differential.
GenevisibleiQ8N3C7. HS.

Organism-specific databases

HPAiHPA043366.
HPA056246.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
JAKMIP2Q96AA84EBI-5655540,EBI-752007
KIFC3Q9BVG83EBI-5655540,EBI-2125614
LZTS2Q9BRK43EBI-5655540,EBI-741037
MAGEA12Q6FHH83EBI-5655540,EBI-10178394
TRIM32Q130493EBI-5655540,EBI-742790
ZNF114Q8NC263EBI-5655540,EBI-10265237

Protein-protein interaction databases

BioGridi122857. 9 interactions.
IntActiQ8N3C7. 26 interactions.
STRINGi9606.ENSP00000327009.

Structurei

Secondary structure

1
705
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi499 – 5057Combined sources
Beta strandi508 – 5125Combined sources
Beta strandi514 – 5229Combined sources
Beta strandi524 – 5307Combined sources
Beta strandi533 – 5364Combined sources
Beta strandi542 – 5465Combined sources
Helixi548 – 5503Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z0WX-ray2.50A482-564[»]
ProteinModelPortaliQ8N3C7.
SMRiQ8N3C7. Positions 84-227, 266-353, 459-697.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8N3C7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati65 – 10137ANK 1Add
BLAST
Repeati149 – 18032ANK 2Add
BLAST
Repeati186 – 21530ANK 3Add
BLAST
Domaini303 – 34543CAP-Gly 1PROSITE-ProRule annotationAdd
BLAST
Domaini505 – 54743CAP-Gly 2PROSITE-ProRule annotationAdd
BLAST
Domaini644 – 68643CAP-Gly 3PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi424 – 47451Ser-richAdd
BLAST

Sequence similaritiesi

Contains 3 ANK repeats.PROSITE-ProRule annotation
Contains 3 CAP-Gly domains.PROSITE-ProRule annotation

Keywords - Domaini

ANK repeat, Repeat

Phylogenomic databases

eggNOGiKOG0241. Eukaryota.
KOG4568. Eukaryota.
COG5244. LUCA.
GeneTreeiENSGT00760000119173.
HOVERGENiHBG057079.
InParanoidiQ8N3C7.
KOiK10423.
OMAiSCQEILF.
OrthoDBiEOG75QR3B.
PhylomeDBiQ8N3C7.
TreeFamiTF326096.

Family and domain databases

Gene3Di1.25.40.20. 1 hit.
2.30.30.190. 3 hits.
InterProiIPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR000938. CAP-Gly_domain.
IPR028397. CLIP4.
[Graphical view]
PANTHERiPTHR18916:SF32. PTHR18916:SF32. 2 hits.
PfamiPF12796. Ank_2. 1 hit.
PF01302. CAP_GLY. 3 hits.
[Graphical view]
SMARTiSM00248. ANK. 3 hits.
SM01052. CAP_GLY. 3 hits.
[Graphical view]
SUPFAMiSSF48403. SSF48403. 1 hit.
SSF74924. SSF74924. 3 hits.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS00845. CAP_GLY_1. 2 hits.
PS50245. CAP_GLY_2. 3 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8N3C7-1) [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
MTIEDLPDFP LEGNPLFGRY PFIFSASDTP VIFSISAAPM PSDCEFSFFD
60 70 80 90 100
PNDASCQEIL FDPKTSVSEL FAILRQWVPQ VQQNIDIIGN EILKRGCNVN
110 120 130 140 150
DRDGLTDMTL LHYTCKSGAH GIGDVETAVK FATQLIDLGA DISLRSRWTN
160 170 180 190 200
MNALHYAAYF DVPELIRVIL KTSKPKDVDA TCSDFNFGTA LHIAAYNLCA
210 220 230 240 250
GAVKCLLEQG ANPAFRNDKG QIPADVVPDP VDMPLEMADA AATAKEIKQM
260 270 280 290 300
LLDAVPLSCN ISKAMLPNYD HVTGKAMLTS LGLKLGDRVV IAGQKVGTLR
310 320 330 340 350
FCGTTEFASG QWAGIELDEP EGKNNGSVGK VQYFKCAPKY GIFAPLSKIS
360 370 380 390 400
KAKGRRKNIT HTPSTKAAVP LIRSQKIDVA HVTSKVNTGL MTSKKDSASE
410 420 430 440 450
STLSLPPGEE LKTVTEKDVA LLGSVSSCSS TSSLEHRQSY PKKQNAISSN
460 470 480 490 500
KKTMSKSPSL SSRASAGLNS SATSTANNSR CEGELRLGER VLVVGQRLGT
510 520 530 540 550
IRFFGTTNFA PGYWYGIELE KPHGKNDGSV GGVQYFSCSP RYGIFAPPSR
560 570 580 590 600
VQRVTDSLDT LSEISSNKQN HSYPGFRRSF STTSASSQKE INRRNAFSKS
610 620 630 640 650
KAALRRSWSS TPTAGGIEGS VKLHEGSQVL LTSSNEMGTV RYVGPTDFAS
660 670 680 690 700
GIWLGLELRS AKGKNDGSVG DKRYFTCKPN HGVLVRPSRV TYRGINGSKL

VDENC
Length:705
Mass (Da):76,317
Last modified:October 1, 2002 - v1
Checksum:i2BE72B2DD2206F12
GO
Isoform 2 (identifier: Q8N3C7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     511-511: P → PVL
     600-705: Missing.

Note: No experimental confirmation available.
Show »
Length:601
Mass (Da):65,177
Checksum:i9400F09A54FE036E
GO
Isoform 3 (identifier: Q8N3C7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     600-705: Missing.

Note: No experimental confirmation available.
Show »
Length:599
Mass (Da):64,965
Checksum:i9628032387B737F4
GO
Isoform 4 (identifier: Q8N3C7-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-150: Missing.
     468-705: LNSSATSTAN...NGSKLVDENC → IYGFFNQAFLVFFILVCLFEFLSNIYSK

Note: No experimental confirmation available.
Show »
Length:345
Mass (Da):37,113
Checksum:i71412DDD803F8983
GO

Sequence cautioni

The sequence BAB14974.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti321 – 3211E → G in BAB14974 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti486 – 4861R → L.
Corresponds to variant rs3100246 [ dbSNP | Ensembl ].
VAR_048675
Natural varianti613 – 6131T → P.
Corresponds to variant rs34327508 [ dbSNP | Ensembl ].
VAR_048676

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 150150Missing in isoform 4. 1 PublicationVSP_012969Add
BLAST
Alternative sequencei468 – 705238LNSSA…VDENC → IYGFFNQAFLVFFILVCLFE FLSNIYSK in isoform 4. 1 PublicationVSP_012970Add
BLAST
Alternative sequencei511 – 5111P → PVL in isoform 2. 2 PublicationsVSP_012971
Alternative sequencei600 – 705106Missing in isoform 2 and isoform 3. 3 PublicationsVSP_012972Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF433661 mRNA. Translation: AAP97312.1.
AK024722 mRNA. Translation: BAB14974.1. Different initiation.
AK057267 mRNA. Translation: BAB71403.1.
AK302325 mRNA. Translation: BAH13674.1.
AL834443 mRNA. Translation: CAD39103.1.
CH471053 Genomic DNA. Translation: EAX00510.1.
BC015310 mRNA. Translation: AAH15310.2.
BC126167 mRNA. Translation: AAI26168.1.
BC136331 mRNA. Translation: AAI36332.1.
CCDSiCCDS1770.1. [Q8N3C7-1]
CCDS74502.1. [Q8N3C7-3]
RefSeqiNP_001274456.1. NM_001287527.1. [Q8N3C7-1]
NP_001274457.1. NM_001287528.1. [Q8N3C7-3]
NP_078968.3. NM_024692.5. [Q8N3C7-1]
XP_005264619.1. XM_005264562.2. [Q8N3C7-1]
XP_005264620.1. XM_005264563.1. [Q8N3C7-1]
XP_006712167.1. XM_006712104.2. [Q8N3C7-1]
XP_011531411.1. XM_011533109.1. [Q8N3C7-1]
UniGeneiHs.122927.

Genome annotation databases

EnsembliENST00000320081; ENSP00000327009; ENSG00000115295. [Q8N3C7-1]
ENST00000401605; ENSP00000384242; ENSG00000115295. [Q8N3C7-3]
ENST00000404424; ENSP00000385594; ENSG00000115295. [Q8N3C7-1]
GeneIDi79745.
KEGGihsa:79745.
UCSCiuc002rmu.5. human. [Q8N3C7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF433661 mRNA. Translation: AAP97312.1.
AK024722 mRNA. Translation: BAB14974.1. Different initiation.
AK057267 mRNA. Translation: BAB71403.1.
AK302325 mRNA. Translation: BAH13674.1.
AL834443 mRNA. Translation: CAD39103.1.
CH471053 Genomic DNA. Translation: EAX00510.1.
BC015310 mRNA. Translation: AAH15310.2.
BC126167 mRNA. Translation: AAI26168.1.
BC136331 mRNA. Translation: AAI36332.1.
CCDSiCCDS1770.1. [Q8N3C7-1]
CCDS74502.1. [Q8N3C7-3]
RefSeqiNP_001274456.1. NM_001287527.1. [Q8N3C7-1]
NP_001274457.1. NM_001287528.1. [Q8N3C7-3]
NP_078968.3. NM_024692.5. [Q8N3C7-1]
XP_005264619.1. XM_005264562.2. [Q8N3C7-1]
XP_005264620.1. XM_005264563.1. [Q8N3C7-1]
XP_006712167.1. XM_006712104.2. [Q8N3C7-1]
XP_011531411.1. XM_011533109.1. [Q8N3C7-1]
UniGeneiHs.122927.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z0WX-ray2.50A482-564[»]
ProteinModelPortaliQ8N3C7.
SMRiQ8N3C7. Positions 84-227, 266-353, 459-697.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122857. 9 interactions.
IntActiQ8N3C7. 26 interactions.
STRINGi9606.ENSP00000327009.

PTM databases

iPTMnetiQ8N3C7.
PhosphoSiteiQ8N3C7.

Polymorphism and mutation databases

BioMutaiCLIP4.
DMDMi60390950.

Proteomic databases

EPDiQ8N3C7.
MaxQBiQ8N3C7.
PaxDbiQ8N3C7.
PeptideAtlasiQ8N3C7.
PRIDEiQ8N3C7.
TopDownProteomicsiQ8N3C7-4. [Q8N3C7-4]

Protocols and materials databases

DNASUi79745.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000320081; ENSP00000327009; ENSG00000115295. [Q8N3C7-1]
ENST00000401605; ENSP00000384242; ENSG00000115295. [Q8N3C7-3]
ENST00000404424; ENSP00000385594; ENSG00000115295. [Q8N3C7-1]
GeneIDi79745.
KEGGihsa:79745.
UCSCiuc002rmu.5. human. [Q8N3C7-1]

Organism-specific databases

CTDi79745.
GeneCardsiCLIP4.
H-InvDBHIX0001941.
HGNCiHGNC:26108. CLIP4.
HPAiHPA043366.
HPA056246.
neXtProtiNX_Q8N3C7.
PharmGKBiPA162382440.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0241. Eukaryota.
KOG4568. Eukaryota.
COG5244. LUCA.
GeneTreeiENSGT00760000119173.
HOVERGENiHBG057079.
InParanoidiQ8N3C7.
KOiK10423.
OMAiSCQEILF.
OrthoDBiEOG75QR3B.
PhylomeDBiQ8N3C7.
TreeFamiTF326096.

Miscellaneous databases

ChiTaRSiCLIP4. human.
EvolutionaryTraceiQ8N3C7.
GenomeRNAii79745.
PROiQ8N3C7.

Gene expression databases

BgeeiQ8N3C7.
CleanExiHS_CLIP4.
ExpressionAtlasiQ8N3C7. baseline and differential.
GenevisibleiQ8N3C7. HS.

Family and domain databases

Gene3Di1.25.40.20. 1 hit.
2.30.30.190. 3 hits.
InterProiIPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR000938. CAP-Gly_domain.
IPR028397. CLIP4.
[Graphical view]
PANTHERiPTHR18916:SF32. PTHR18916:SF32. 2 hits.
PfamiPF12796. Ank_2. 1 hit.
PF01302. CAP_GLY. 3 hits.
[Graphical view]
SMARTiSM00248. ANK. 3 hits.
SM01052. CAP_GLY. 3 hits.
[Graphical view]
SUPFAMiSSF48403. SSF48403. 1 hit.
SSF74924. SSF74924. 3 hits.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS00845. CAP_GLY_1. 2 hits.
PS50245. CAP_GLY_2. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Guo J.H., Yu L.
    Submitted (OCT-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
  2. "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] (ISOFORM 3), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 102-705 (ISOFORMS 3 AND 4).
    Tissue: Testis.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Amygdala.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 48-705 (ISOFORM 2).
    Tissue: Lung and Prostate.
  6. "Crystal structure of the 2nd CAP-Gly domain in human restin-like protein 2 reveals a swapped-dimer."
    RIKEN structural genomics initiative (RSGI)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 482-565.

Entry informationi

Entry nameiCLIP4_HUMAN
AccessioniPrimary (citable) accession number: Q8N3C7
Secondary accession number(s): A0AV10
, B2RMQ3, B7Z7N8, Q7Z4U3, Q96BR7, Q96MA5, Q9H7C0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: October 1, 2002
Last modified: July 6, 2016
This is version 114 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. 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.